Wales, who ground out a 17-0 win in the opening Test, had the better of the early exchanges.
They were rewarded with the opening try after Japan’s loose goalline drop-out, which co-captain Alex Callender thundered up deep into the 22.
Tuipulotu then came close, before the ball was shipped to Metcalfe to finish in the corner. Lleucu George, preferred at 10 this week to Bevan, added the conversion.
The hosts then enjoyed a spell of pressure thanks to Wales’ indiscipline and bagged their first try of the double header with hooker Nagaoka touching down from the maul.
Wales were back among the tries 10 minutes later with George’s kick putting the defence under pressure and Lisa Neumann winning the turnover.
Wales rightly backed their line-out with Jones touching down for her second in as many games. George was again on target from the tee to extend Wales’ lead.
Despite improved conditions this week, the visiting backline looked a little disjointed, but the maul was dominant and Japan could do little to stop it from gaining ground before Seren Lockwood found Williams in space on the wing.
Japan’s indiscipline proved costly in the second half, with Jennifer Nduka paying the price for an accumulation of penalties with a yellow card.
It paved the way for Wales to cross for the try bonus-point, with Tuipulotu proving unstoppable from a metre out.
Wales continued to play through the forwards, with Callender working tirelessly in her new position of eight this week.
The backs eventually got in the action and it came from a huge Callender pass out wide to Neumann who fed the pacy Williams for her second run in of the evening.
Both sides emptied their bench soon after, and while Wales’ replacements proved the difference last weekend, it had the opposite effect this week, with the experienced Bevan and Dallavalle both shown yellow cards as the game entered its final 10 minutes.
Bevan had been penalised when Wales had been on a warning, while Dallavalle, making her first appearance in the competition, was given her marching orders for a blatant hair pull.
Japan threw everything at Wales in the dying moments, but could not take advantage of their numbers and it was fitting that Callender came up with the crucial turnover.