Faddes touched down twice in an eight-minute burst after half-time as the 2015 champions notched their fourth straight win to shore up their place in the playoffs berths.
Malakai Fekitoa, Liam Squire, Aaron Smith and Ben Smith also crossed, with Marty Banks converting five of the home side's six tries.
After an early penalty by flyhalf Yu Tamura, the Japanese visitors were kept scoreless for nearly 50 minutes but grabbed consolation tries to Willie Britz and Rahboni Warren-Vosayaco late in the game.
Appearing in disarray after the opening rounds of the season, the Highlanders have now clicked into gear and their potent backline cut the Sunwolves to pieces in the middle part of the match.
Coming off a bye, they were rusty early and were kept scoreless in the last quarter, leaving captain Ben Smith feeling lukewarm about the performance ahead of a crunch match against the Cape Town-based Stormers.
"It wasn't perfect and at times we threw a few miracle balls and didn't show them the respect, so there's a bit to work on," Smith said.
"We've got a home game (next) against the Stormers so we'll have to fix a few things up."
The Sunwolves were on the back foot from the third minute, with a bungled line-out leading to a turnover and inside centre Fekitoa crossing for the first try after being put into a hole by winger Waisake Naholo.
Ben Smith put the last points on the board for the Highlanders with a pick-and-go try before the Sunwolves' late rally.
Number eight Britz broke through the Highlanders' line deep in attack and shrugged off a tackle to cross for the Sunwolves' first try.
Replacement loose forward Warren-Vosayaco later touched down at the right corner after collecting a neat, lofted pass from Tamura.
(Reporting by Ian Ransom in Melbourne; Editing by Amlan Chakraborty)
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