Double world champion Fernando Alonso put on a characteristically dogged drive through the field to finish 11th but was handicapped from the start by a 35-place engine-related grid penalty.
The Spaniard was also handed a reprimand and two penalty points for ignoring blue flags instructing him to get out of the way of front-running cars.
His Belgian team-mate Stoffel Vandoorne started ninth but dropped down the field after contact on the opening lap to finish 14th.
"This is our home grand prix, so we obviously have very strong feelings for this race," said the Japanese manufacturer’s Formula One chief Yusuke Hasegawa at the Honda-owned Suzuka circuit.
"I want to say a huge thank-you to all of the fans that turned out to support us and also to the team who worked tirelessly throughout the weekend.
"It is a shame they weren’t rewarded with any points, but we still have four races left this season and we’ll continue to battle to the end."
McLaren and Honda, who dominated Formula One in the late 1980s, are separating at the end of the season.
The pair have failed to recreate the glory days of Ayrton Senna and Alain Prost and the three seasons since they rekindled their partnership have been marked by dismal performances, largely due to a lack of engine power and reliability.
McLaren, ninth out of 10 teams in the overall standings, will switch to Renault next season with Toro Rosso, currently powered by the French manufacturer, picking up the Honda supply.
McLaren chalked up consecutive points finishes in the last two races in Singapore and Malaysia, with Vandoorne seventh in both, and would have hoped to equal their previous best streak of three successive points finishes.
"Still, on the whole, this Asian triple-header has been a positive one for the whole team," said McLaren racing director Eric Boullier.
"We’ll definitely put that momentum to good use in the final four races."
(Editing by Alan Baldwin and Toby Davis)
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