Manly moved back into the top six with the win while the Raiders are languishing four from the bottom with just three wins for the season.
Stewart staked a claim for State of Origin selection and kept Manly in the match with three try-saving tackles, the last with Manly leading 16-12 and 20 minutes still to go.
“I don’t think there was any great attacking displays today but the defence was very tough,” Manly coach Geoff Toovey said.
“I thought our defence on the line and our last-ditch efforts to save tries was outstanding, particularly from the fullback (Stewart)”.
The Sydney Roosters also moved back into finals contention, beating Newcastle 24-6.
Sydney coach Brian Smith paid tribute to the performances of his lesser known players, singling out Mose Masoe for special praise as his side bounced back from a loss last round to climb into the top eight.
“I’ve never seen Mose have a game like he did today, he was our catalyst,” Smith said. “We are working hard to play grinding footy and reduce errors and that was largely on the back of our lesser lights.”
The Melbourne Storm stayed on top of the table and remained unbeaten after their dominant 44-10 win over Penrith on Saturday. However, second placed Brisbane Broncos slipped up when they were beaten 30-20 by New Zealand Warriors in Auckland.
In other matches Tigers squeezed past Titans 15-14, Cowboys moved to fourth place with a 30-6 win over St George and Canterbury thrashed the lowly Parramatta Eels 46-12.