Stewart was carried from the field just before halftime in another epic contest between the bitter rivals, his left knee twisting awkwardly under the weight of Storm utility Rory Kostjasyn.
The initial diagnosis was a strained medial ligament and a layoff of between 2-4 weeks - leaving him next to no chance to play the Origin decider in Brisbane on July 4.
It was Stewart's first game against the Storm on the northern beaches since last year's spiteful encounter, when his sideline scuffle with Adam Blair sparked a wild all-in brawl and cost him a three-match ban.
There were no fists thrown on Monday night and it didn't detract from an enthralling contest between the two most dominant sides of recent years.
It was only settled when Cameron Smith edged the runaway ladder-leaders ahead by more than a converted try with a penalty goal nine minutes from time.
In a match punctuated by momentum swings, the Storm jumped out to an early 12-0 lead through tries to Todd Lowrie and Smith - the latter coming after a feeble attempted tackle by Anthony Watmough.
A controversial call by video referee sparked a turnaround in the home side's favour - 18 points in 12 minutes started when Daly Cherry-Evans was awarded a try after the man in the box Paul Simpkins ruled Ryan Hoffman had knocked the ball from his grasp as the Manly No.7 attempted to ground the ball.
Brett Stewart and Jorge Taufua added their name to the scoreboard for a 18-12 halftime lead, but given the ferocity of their comeback, Manly's surrender of their lead was surprisingly meek.
Bryan Norrie was the most urgent to get to a loose ball after a scrambled piece of play when Melbourne ran it on the last, but it was all precision as they regained the lead when Matt Duffie flew highest to reel in Cooper Cronk's cross-field kick - Dean Whare cutting the deficit 30 seconds from fulltime.