Nick Timoney, Tom O'Toole, Robbie Henshaw and Tom Stewart were responsible for Ireland's other tries at McDonald Jones Stadium in Newcastle on Saturday.
Ciaran Frawley kicked for six points and Harry Byrne for four to ensure Ireland remained top of the northern hemisphere group.
Ireland head coach Andy Farrell made nine changes after their narrow win over Australia, with Tadhg Beirne captaining for the first time and hooker Ronan Kelleher reaching a half-century of caps.
No.8 Jansen started, while his Connacht teammates Billy Bohan and Sam Illo were also handed debuts off the bench, alongside Ulster back-rower Bryn Ward.
It didn't take long for Japan to strike, capitalising on an error-strewn Ireland lineout that allowed Taira Main to run in their first try in the third minute.
Ireland hit back six minutes later, keeping the pressure on after Henshaw took a big hit, and were rewarded when Timoney drove between the posts.
There was another poor lineout from Farrell's side before Takuro Matsunaga pulled Japan back in front with a penalty, then Ireland took the lead when O'Toole crossed the whitewash in the 20th minute, aided by Stuart McCloskey.
The lead switched again when Matsunaga added a second penalty, but it was 19-13 to Ireland after Henshaw powered over with six minutes remaining in the first half.
Illo came on for his debut in a double change for Ireland, who started the second half more clinically as fellow replacement Bundee Aki justified his introduction, latching on to a Henshaw pass.
His run got Ireland close, but it was Jansen who finally finished the job and secured the bonus point in the 50th minute.
Japan kept it a contest, taking advantage again after Ireland let themselves down from the lineout, paving the way for substitute hooker Hayate Era to battle his way to a try two minutes before the hour.
Byrne added a much-needed cushion with a penalty to make it 29-20 with 10 minutes remaining.
Japan were reduced to 14 men when Era was sent off with three minutes remaining, before Stewart, set up brilliantly by Ulster teammate Nathan Doak, sealed the win.
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