Hamilton was .199 seconds faster than Bottas in cool, overcast conditions, followed by the two Red Bulls of Max Verstappen and Daniel Ricciardo.
It's the second season in a row that Vettel has started strongly only for Hamilton to surge in the second half.
Vettel sat glum-faced in the news conference after qualifying third, trailing Hamilton by a sizeable margin in Formula One terms: 0.6 seconds.
Sebastian Vettel was nearly two seconds behind Raikkonen in ninth, but was using slower tires than his teammate.
Vettel and Hamilton are both chasing a fifth F1 title to move level with Argentine great Juan Manuel Fangio and go two behind record-holder Michael Schumacher.
The Mercedes driver beat Raikkonen, who had started in pole, to tie Michael Schumacher's record of five Italian GP victories and extend his championship lead.
Surprisingly, it was Kimi Raikkonen who edged his teammate and title hopeful Vettel in qualifying on Saturday to clinch only his second pole position in 10 years.
Hamilton started from pole position for a record fifth time at Spa, and a record-extending 78th in Formula One, with Vettel second on the grid.
Raikkonen was .168 ahead of Hamilton and nearly a half second clear of the British driver's Mercedes teammate, Valtteri Bottas.
Vettel lost his way after the summer break last year, winning only one of nine races compared to five by Hamilton.
Hamilton was untroubled as he secured a second straight win, fifth of the season and 67th overall.
Vettel was faster than Red Bull drivers Max Verstappen and Daniel Ricciardo.
Vettel should have been the one in the ascendancy, but his clumsy crash while leading the rain-soaked German GP last Sunday cost him the race and gifted victory to Hamilton.
Hamilton's love of fighting from the back is somewhat ironic, considering he is F1's record holder with 76 pole positions — eight more than Michael Schumacher.
Leading both the drivers' and constructors' championships before the race, Vettel and Ferrari are now behind in both.
The German's mishap opened the door wide open for Hamilton, who is 17 points clear of Vettel after trailing by eight beforehand.
Already trailing Vettel by eight points in the title race, Hamilton starts Sunday's race from 14th place after a hydraulic failure.
Hamilton managed to fight his way back to finish second after a Ferrari-Mercedes duel developed with Valtteri Bottas leading until Vettel hit the front again with five laps to go.
Hamilton, who is going for a fifth straight victory and a record sixth overall in his home Formula One race, clocked the best lap time at 0.367 seconds faster than Bottas.
Bottas edged Hamilton by 0.019 seconds for his first pole position of the season as Mercedes locked up the front row of the grid for the third time this year.
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