Mr Javid, the son of Pakistani Muslim parents, was the only holder of a great office of state - which include prime minister, foreign secretary, home secretary and chancellor - not to be invited to the opulent dinner hosted by the Queen.
The omission of the Conservative leadership hopeful from the guest list has raised eyebrows in Westminster, as rivals Jeremy Hunt, the foreign secretary, and Michael Gove, the environment secretary, were among senior ministers in attendance.
Mr Javid previously condemned the president for sharing Islamophobic tweets from the far-right extremist group Britain First in 2017.
His allies were unconcerned by the snub, joking that he may have been left off the list because he had been confused with Sadiq Khan, the Labour mayor of London, who is also of Pakistani heritage.
"Maybe Downing Street was worried the president might confuse him with the other son of a bus driver," a friend told the Daily Mail.
The president has a long-running feud with Mr Khan. His first act on arriving in London was to brand the mayor a "stone cold loser" after Mr Khan accused him of whipping up his followers with the rhetoric of "20th Century fascists".
Mr Trump tweeted: "Sadiq Khan, who by all accounts has done a terrible job as mayor of London, has been foolishly "nasty" to the visiting president of the United States, by far the most important ally of the United Kingdom.
"He is a stone cold loser who should focus on crime in London, not me."
The state banquet is one of the key events of the president's three-day visit, with 170 guests drawn from the royal family, industry and political life.
Politicians at the event included Theresa May and her husband Philip, de-facto deputy PM David Lidington, Philip Hammond, the chancellor, defence secretary Penny Mordaunt, Michael Gove, the environment secretary, and international trade secretary Liam Fox.
The guest list for the state banquet was determined by Buckingham Palace, with input from the government and also from the American embassy. Invitations are issued by the Lord Steward on behalf of the Queen.
A Downing Street spokesperson said: "The invitations to the state banquet were organised and led by Buckingham Palace."
In her speech, the Queen delivered what could be seen as a coded rebuke to Mr Trump over his criticism of international institutions created after the Second World War to ensure peace, such as Nato and the UN.
"As we face the new challenges of the 21st Century, the anniversary of D-Day reminds us of all that our countries have achieved together," she said.
"After the shared sacrifices of the Second World War, Britain and the United States worked with other allies to build an assembly of international institutions, to ensure that the horrors of conflict would never be repeated.
"While the world has changed, we are forever mindful of the original purpose of these structures: nations working together to safeguard a hard won peace."
Mr Trump praised the Queen for her "spirit of dignity, duty, and patriotism that beats proudly in every British heart", after he spent the day with the "fantastic" royal family.
The president is expected to press Ms May to block Chinese tech giant Huawei out of the UK’s 5G telecoms network during talk at Downing Street on Tuesday.
Brexit and trade will also be high on the agenda in his discussions with Ms May, who will co-host a meeting of British and US business leaders in St James’s Palace.
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