Stewart was hurt when his right knee jammed into the hard Marvel Stadium surface on Saturday night as the Saints held off their fast-finishing opponents to prevail 15.8 (98) to 13.13 (91).
The five-time All-Australian was substituted out before halftime, adding to the Cats' woes after Bailey Smith (calf) was a late withdrawal.
St Kilda defied their own long injury list to bounce back from a round-one thumping by Adelaide, kicking as many as 41 points clear during the third term.
Geelong stormed home with seven of the last nine goals, but were held off by a spirited Saints outfit.
Jack Macrae (35 disposals), Zak Jones (27) and Nasiah Wanganeen-Milera (29) were all influential for St Kilda, and Jack Higgins was the best of their goalkickers with four.
Marcus Windhager blunted Cats star Max Holmes in the first half and finished with 25 disposals and two goals, and Rowan Marshall fought tirelessly in the ruck.
There was some concern for the Saints, who lost Liam Stocker to concussion before halftime.
Geelong, who thrashed Fremantle by 78 points at home in round one, were made to look second-rate in the first half against the Saints.
They lifted late in the contest, with Patrick Dangerfield (18 disposals) and Ollie Dempsey (two goals) providing final-quarter sparks.
But Dangerfield faces scrutiny from the match review officer over a high elbow that clipped Ryan Byrnes as he kicked the ball.
Two Saints players immediately remonstrated with Dangerfield after the third-quarter incident.
In a stunning start to the match, St Kilda piled on six goals to one in the first quarter, and the Cats held their collective breath when Stewart limped off.
The star defender briefly returned with his right knee strapped after quarter-time, but could not continue.
The Saints' lead ballooned to 40 points when Higgins slotted his third goal, but two late Geelong goals trimmed the margin to 29 by halftime.
St Kilda kicked the first two goals of the second half, including one to debutant Isaac Keeler, but coughed up four of the next five.
Dangerfield was huge in the final term and Geelong kicked 4.4 to 1.2 but ran out of time to complete what would have been a remarkable comeback.
St Kilda will fancy their chances against Richmond at Marvel Stadium in round three, while Geelong face a tough test against reigning premiers Brisbane at the Gabba.
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