Yet, former New Zealand great Andrew Mehrtens labelled the performance a "backwards step" in commentary midway through the second half.
So abject was their second-half performance Quade Cooper, who was excellent in the opening half, was forced to look for a penalty to extend their lead out beyond a converted try late in the match.
But Cooper, who kicked Australia to victory against South Africa a month earlier to start their excellent run of form, kicked wide.
Soon after Japan was awarded a penalty.
Rather than going for the try to level up the match, they opted for a shot at goals so they could win the ball back and mount a late surge to try and steal the match at the death.
It was another sign of how far the Brave Blossoms have come since Eddie Jones led Japan to the World Cup's greatest upset in 2015, as his side went for the winning try against the Springboks rather than electing for a simple goal that would have given them a stunning draw.
Yu Tamura landed the penalty to cut the margin to 27-23, but Japan failed to turn the pressure into an upset win as replacement hooker Connal McInerney had a dream debut by scoring the match-sealing try.
The Wallabies leave Japan for England on Sunday, where they will set-up camp in Brighton for the week before leaving for Edinburgh before their Test against Scotland at Murrayfield.
They will be sweating on the fitness of fullback Reece Hodge, who is set for scans after being forced off early with a suspected pec injury.
His injury further reduces Rennie's fullback stocks, with Hodge moving to the position after Tom Banks was earlier ruled out of the rest of the year with a fractured arm suffered against South Africa.
Should Hodge miss the Novembers Tests, it is likely Andrew Kellaway, who shifted from his wing to fullback, will cover the position but calls must be sounding for Kurtley Beale to drafted into the squad from Paris.
The Wallabies made a bright start off the back of some Cooper magic.
From a dominant scrum, Rob Valetini powered his way into the 22 metre line after a lovely inside ball from Cooper.
Soon after, the Wallabies playmaker stepped off his inside, broke the line and offloaded to a free-running Tom Wright to score inside the opening 10 minutes.
It was just the statement run that Cooper needed to show after an understated return to Test rugby, where his decision-making and distributing had been on show.
Japan managed to get on the board after Kellaway failed to release the ball after being tackled.
But the Wallabies extended their lead when Cooper and Kellaway sent Petaia into score after finding space from a rolling maul to see the visitors race out to a 14-3 lead midway through the opening half.
An Izack Rodda mistake from the kick restart however provided Japan an opportunity to strike back.
After a patient, 10-phase build-up, they did just that as winger Lomano Lemeki scored after 25 minutes off the back of a sublime cross-field kick from playmaker Rikiya Matsuda.
Matsuda reduced the deficit to 14-13 with his second penalty, before Cooper landed a simple shot on goals after Rob Leota made a surging run down the right-hand touchline to get the Wallabies over the gain line.
Once again the Wallabies burst out of the blocks following a clever set-piece lineout play which saw Taniela Tupou barge his way over.
A careless shoulder charge from Lemeki on Hunter Paisami, who struggled to fill the shoes of Samu Kerevi, allowed the Wallabies to go a man-up.
And following some razzle dazzle from Wright, Nic White and Cooper, Leota scored a stunning try.
Rennie rang the changes soon after hoping to finish the match with some authority.
All it did, however, was continue their theme of poor finishes, as Cooper threw an intercept which was superbly read by Ryoto Nakamura.
Tamura's gave the Wallabies a real freight when he landed his penalty in the 74th minute.
It was then Rennie finally injected James O'Connor, who had curiously been left on the sidelines despite Tate McDermott's earlier arrival.
A fantastic piece of work from Rob Valetini in the outside channels on the ball allowed the Wallabies to kick for the corner.
It ended with debutant McInerney scoring to continue his love-affair with Japan, having previously scored a hat-trick against the Sunwolves in Super Rugby.
