The Sea Eagles, who secured their fourth win, set the win up with an 18-point first half, which included a brace of tries to winger Jorge Taufua.
Stewart laid on two tries in a sublime first half to put his name forward to retain the Blues No.1 jersey.
Stewart helped open the scoring when he threw a beautiful cut-out pass for Taufua's opening try before the disappointing crowd of 18,563 after just eight minutes.
Soon after Stewart produced a scything 35-metre run before linking up with Jamie Lyon, who sold a dummy and snuck past four Bulldogs defenders to score next to the posts.
Lyon kicked four from five, including a penalty which constituted Manly's only second-half points, for a personal haul of 12 points.
Manly's forward pack, led by a stellar performance from Anthony Watmough, completely outmuscled a Canterbury pack desperately missing star props Sam Kasiano (leg) and James Graham (suspension).
The Bulldogs were uncharacteristically sloppy, making seven first-half errors and regularly inviting Manly into their red zone.
The hosts scored a consolation try to captain Michael Ennis with eight minutes to go, but it is unlikely to be enough to placate coach Des Hasler.
Imposing Bulldogs second-rower Tony Williams continued his lacklustre start to the season - making just 51 metres in his first match against his former club.