Forwards coach O'Donovan, on head coach watch due to Eddie O'Sullivan's involvement with the Lions in New Zealand, had clearly done his homework as the tourists outscored the Japanese by four tries to none.
Having opened well with two penalties from stand-in skipper David Humphreys and a try from Ulster wing Tommy Bowe, the Irish went on, despite the loss of steadying fly-half Humphreys to a heavy head blow on 21 minutes, to bag further tries from 70-cap centre Kevin Maggs before the break, and front rowers Frankie Sheahan and Simon Best in the closing quarter.
Best's effort - his first for his country - was the highlight as Irish backs and forward kept the ball-in-hand, shipping some heavy hits from the tireless Japanese to set up the Ulster prop's 69th-minute score.
The home side, who lost the Super Cup final 15-10 to Canada last time out, scored four penalties from the boot of fly-half Kyohei Morita before their challenge wilted with the second half sin-binning of record try scorer Daisuke Ohata.
"We're very pleased with the win. We played some good stuff, kept it tight, scored our tries and defensively, it's was a bonus to keep them out for the full eighty minutes," said O'Donovan afterwards.
"Japan played as we expected them to play. They were competitive in all aspects of play, particularly at the breakdown.
"Our players haven't played for a few weeks and competed well to the end though."
The game, Japan's seventh Test outing in little over two months, was also notable for six players - Matt McCullough, Roger Wilson, Bernard Jackman, David Quinlan, Trevor Hogan and Kieran Campbell - making their senior Ireland debuts.
Ireland team manager Joey Miles added: "To get six players off the mark at international level and score four tries away from home was particularly pleasing, although the game lacked any real pattern.
"It was hard to maintain any sort of stronghold in the conditions but I thought we did well in the first half to soak up the Japanese pressure."
The two side meet again next Sunday in Tokyo, and Japanese skipper Takuro Miuchi has already promised that his side will "go out to win at all costs."
Japanese coach Mitsutake Hagimoto conceded: "The result is very disappointing but the players did well.
"We are building to the 2007 World Cup and the hope is to be a top-eight nation by 2011 so we need games like this."