Lonsdale was born in 1905 and in 1919 joined the Royal Navy. He entered the Trade, as the submarine branch of the service is known, in 1927 and within four years was First Lieutenant of XI, the enormous experimental submersible with her four 5.2-inch guns and displacing 2,780 tons - by far the biggest craft before the nuclear boats. In 1934 he passed the submarine command qualifying course, so demanding that it is known as the Perisher.
His first command was H44, a legacy of the Great War, of 440 tons, with four torpedo tubes and a machine-gun; in 1937 he took over the newer Swordfish for a year. His next command, Seal, 1,520 tons, was being built in Chatham Yard - she had a 4-inch gun and two machine-guns, and was the last of six boats designed primarily as minelayers: only one survived the war.
Lonsdale was promoted Lieutenant-Commander in May 1936; one of his contemporaries was David Luce, later First Sea Lord. His wife, Christina Lyall, died in September 1937, giving birth to a son John, their only child; the bereaved father was appointed to Seal in command on 1 November 1938 and commissioned her in May 1939. On 4 August she sailed for the China station; within a month she was at war, detained at Aden whence she made two ad hoc patrols watching the Italians.
Back in home waters she did one North Sea patrol before an unexpected 14-day crossing to Halifax, Nova Scotia, augmenting a convoy escort in case it attracted an attack - an unusual and questionable role for her class. She got home in time to grant Christmas leave and then, based at Elfin, a temporary establishment at Blyth, settled to a North Sea patrol routine soon dominated by the Norwegian campaign.
Her last mission was to transit the Skagerrak and lay a minefield in the Kattegat. This was a hairy prospect for any boat; for one as big as Seal it was particularly daunting. Lonsdale's captain failed to persuade Admiral Horton, a legendary submariner himself, to reconsider his orders and on 29 April Seal sailed.
She found German trawlers sweeping her target area, laid low on the bottom to await their departure, but exploded a German mine which damaged her stern. Her hull began to fill. Lonsdale decided not to abandon ship by using the Davies escape gear, but to try and make for the nearby Swedish coast.
He managed to reach the surface but enemy aircraft strafed the conning tower, summoned patrol craft and kept the boat under attack. The crew were exhausted by fumes and there was no realistic alternative to surrender; an attempt to scuttle the boat failed. Early on 5 May 1940, his 35th birthday, Lonsdale swam to a seaplane and into captivity. He had done all that could be done but he never forgave himself. Ironically, he was mentioned in despatches four days later for his previous patrol work.
His fame as a captain is secure. His quiet and considerate approach to command succeeded to an unusually high degree. His men knew something of his steady reputation from his previous command; most were aware of his bereavement. The few critics or doubters soon found themselves converted to the admiring majority, for Lonsdale was firm but fair to all. He never sought popularity, or lost his temper. He was no piratical extrovert, no swashbuckler. Many of his orders sounded like civil requests. "Sixty feet!" - the captain's order to submerge - was usually "Sixty feet, please, no 1".
During his five long years of imprisonment, Lonsdale enjoyed the respect of his captors and found increasing comfort in his Christianity. But he was inconsolable. As the inevitable court-martial loomed with liberation (anyone who loses or hazards a ship is court- martialled), "his modesty was such that he had not begun to realise that there was even the slightest possibility of his being considered not as a coward but as a hero".
Lonsdale's agony would have been assuaged had he received two signals made by Horton in response to his surfacing signal giving his intention to make for Sweden - "Understood and agreed with. Best of luck. Well done." This was followed by "Safety of personnel should be your first consideration after destruction of Asdics [an anti-submarine device]". Alas, they did not get through.
Six years after Seal had become UB in the German navy - her only intelligence value being a certain amount of information about her torpedoes - Lonsdale was tried at Portsmouth, on 10 April 1946; it took the court just over half an hour to acquit him. He was mentioned in despatches in June that year for his services as a POW, promoted Commander and placed on the Retired List at his own request.
His last command had been the new Algerine-class fleet minesweeper Pyrrhus, which he had worked up from Glanton before joining an operational flotilla at Portsmouth in January 1946. With the exception of the Engineer Officer, his wardroom was entirely RNVR; again, there was that rapport with the ship's company. They knew he had leave accruing from his time as a POW, and were not surprised at his quiet departure until they read in the newspapers of his trial and acquittal.
Lonsdale went to Ridley Hall in Cambridge in 1946 to prepare for his ordination; he became a priest in 1949. His first curacy was with a mission church at Rowner, significantly perhaps near Dolphin, the submarine base at Gosport. He was vicar of Morden-with-Almer in Dorset from 1951 to 1953 and then spent five years in the White Highlands of Kenya as a District Chaplain.
He volunteered for this mission because he thought that his own five years as a prisoner should help him to befriend the Mau Mau rebels, with whom at one point he offered to live in the bush as a hostage, as evidence of Britain's benevolent intentions. He went back to England to be Vicar of Bentworth-with-Shaldon in Hampshire (1958-60) but then returned out of affection to Kenya for another tour of duty. Now a Canon Emeritus, his last full-time incumbency was Vicar of Thornham-with-Titchwell (1965-70) on the north Norfolk coast, near to Nelson's birthplace in his father's parish of Burnham Thorpe.
Lonsdale then retired to Hampshire, and among several part-time chaplaincies for the Church's European diocese based on Gibraltar was a three-year stay in Tenerife (1970-73) before he returned to England for some time in the College of St Mark at Audley End, until it ceased to be a clergy hospice.
He was married three times after the war, first to Kathleen Deal, whom he took out to Kenya, and who died in 1961, then to Ursula Sansum, of whom he first knew as a WRNS officer, who also supported him in Kenya (she died in 1986), and finally to Ethne Irwin, whom he married in 1989 in Malta, and with whom he returned to England in 1996. She survives him, as does his son John Lonsdale, Fellow of Trinity College, Cambridge, who spent his National Service on secondment to the King's African Rifles in Kenya before specialising in East African history.
In 1960 Rupert Lonsdale was asked by C.E.T. Warren and James Benson for his help with their book about the loss of Seal, Will Not We Fear (1961). He eventually agreed, provided that he was allowed to write a foreword making it clear that he would never have suggested that the book be written, that he was a reluctant contributor, and then only in the trust that it might help some readers to find faith in God: "Now that the tale is written I recoil all the more from any publicity, but the one reason for my co- operation remains." There is also a simple but eloquent tribute from him to his ship's company.
The authors saluted him by prefacing his foreword with the first seven verses of Psalm xlvi from which they drew their title.
Rupert Philip Lonsdale, naval officer and priest: born Dublin 5 May 1905; ordained deacon 1948, priest 1949; married 1935 Christina Lyall (died 1937; one son), 1953 Kathleen Deal (died 1961), 1963 Ursula Sansum (died 1986), 1989 Ethne Irwin; died Bournemouth, Dorset 25 April 1999.