Saito took 52 days, twice as long as the leg winner, the Italian Giovanni Soldini, to complete the 7,000 miles (11,000 km) from Cape Town to Auckland.
Along the way he celebrated his 65th birthday and remains on course to become the oldest sailor to complete the race.
The fact his 50ft yacht, the Shuten-dori, was a little smelly on arrival in Auckland harbour was blamed on a freezer that broke down 15 days out from South Africa.
"I had many meats - chicken, pork, beef, tuna. They all go off. I have a very, very bad smell on board now," said Saito, whose priority on stepping ashore was a cold beer.
However, the problem did not worry the veteran yachtsman, who has survived five heart attacks and has sailed around the world twice since selling his Tokyo petrol station 14 years ago.
Saito reached Auckland at midday and was followed in six hours later by the 31-year-old South African Neal Petersen.
Fifteen yachts set off from Cape Town on 5 December and disqualification faces the three boats that are still on the water. The cut-off point is noon tomorrow and Britain's Robin Davey has no chance of making Auckland in time - he still has 1,200 miles to go. The other two are the Russian Fedor Konioukhov and the Australian Neil Hunter.
The race is led by the only woman taking part, France's Isabelle Autissier. The fleet is due to leave Auckland on 6 February for Uruguay, en route to a finish in Charleston, South Carolina.Reuse content