McLaren's Oscar Piastri finished third with Red Bull's championship leader Max Verstappen fifth after starting 11th on the grid.
Hamilton looked set to win his fifth Belgian GP after he outfought Red Bull's Sergio Perez at the start to move into second and took the lead on lap three, overtaking Ferrari's Charles Leclerc, who finished fourth, on the Kemmel straight.
Russell started sixth on the grid and came in for his first pit stop on lap 10 with Hamilton coming in two laps later, but while Hamilton came in again on lap 27, Mercedes were happy for his teammate to stay out until the end.
"Amazing, amazing result, definitely didn't predict this win this morning in our strategy meeting," Russell said.
"The tyres felt great so I just kept saying we can do the one-stop, we can do the one-stop. Well done to Lewis, he did a great job controlling the race and if circumstances were different he could have won the race."
Hamilton closed the gap in the final laps but could not get close enough to overtake Russell and finished 0.526 seconds behind his teammate, who won his second race of the season.
While neither Mercedes driver is in the hunt for the Championship, Hamilton may feel slightly aggrieved.
"I was trying to get closer obviously, but George did a great job going long on the tyres," Hamilton said. "Every stint I had tyres left but the team brought me in, so unfortunate, but it is one of those days."
RACING BREAK
Piastri, fresh from his Hungary success, came in 1.173 seconds behind the leader, and his final pit stop where he ran over his marks cost him two precious seconds.
Leclerc, who started on pole, had to settle for fourth ahead of Verstappen, as the triple world champion failed to win for the fourth straight race, the first time since 2020 that has happened.
Red Bull took the engine penalty, as they did the last two years at Spa, but this time Verstappen was unable to muscle his way through the field and missed out on winning in Belgium for a fourth successive season.
Lando Norris, second in the drivers' championship, came in sixth for McLaren with Ferrari's Carlos Sainz seventh. Perez failed to take advantage of his start on the front row and finished eighth, but did post the fastest lap.
Aston Martin's Fernando Alonso was ninth with Alpine's Esteban Ocon, who will drive for Haas next season, finishing 10th.
Mercedes have now won three of the last four races, and they closed the gap in the constructor's championship to third placed Ferrari to 56 points.
The season now takes a four-week break, and while Verstappen extended his lead over Norris to 78 points, his dominance of last year is well and truly over.
In 2023 Verstappen lost only three races all season, but has already failed to win seven of 14 this year, with 10 races to come.