But it was very nearly Scottish driver Paul Di Resta who grabbed top spot in qualification after making a "ballsy" call at the start of the session.
The nine other drivers had opted for slick tyres, but Di Resta chose intermediates as he spotted umbrellas going up in the stands.
As the rain slowly fell, forcing his rivals back into the pits to switch tyres, Di Resta posted a time to put him at the top of the pile.
"I thought the rain was going to stay. It was quite a ballsy decision by myself. I saw umbrellas so I made the right choice," said Di Resta, who ended up fifth-fastest - his highest qualifying position - in his Force India after the rain passed, allowing Nico Rosberg, Mark Webber, Sebastian Vettel, and Hamilton, to achieve faster drives.
"It is a great result. It's a shame the rain stopped a bit too early because there were only a few cars quicker than us in the wet, and they just got ahead at the end of the session.
"Our car is not that quick in the wet. It was unfortunate, but P5 is not so bad. In the dry, we're looking good for the race. If it's wet, I'd be a bit more nervous."
Hamilton, however, as the last man out, was the main beneficiary of the changeable weather over the Spa-Francorchamps circuit as he became the first Briton since Damon Hill in 1995 to collect four poles in a row.
The dry line which appeared in the third session proved crucial to the 28-year-old.
"It's absolutely fantastic, a great feeling. I feel very privileged to have a car to be able to do that," said Hamilton of his Mercedes. "It's cool to have done something similar to one of the greats, and who would have thought? The year just seems to be getting better and better.
"It's just amazing to think we've come here with a car where we know we can be competitive and, for whatever reason, I was able to put it out there. We're going to try and work as hard as we can to beat both the Red Bulls. It's not impossible. We just have to get our strategy right.
"I was so surprised when I crossed the line. When I started the lap I saw I was about seventh or eighth, and I thought 'Oh my God', especially as it was raining more. I then went wide in turn one and the dash display told me I was three seconds down, then five seconds and six seconds. I didn't understand what was happening in the lap, but I kept pushing. I could see I was catching Sebastian towards the end."
Hamilton will have both Red Bulls behind him, with Vettel ahead of team-mate Webber for the 11th successive race this year and the Mercedes driver's own team-mate, Rosberg, fourth on the grid.
Jenson Button grabbed a season-best sixth in his McLaren, while title contenders in Lotus' Kimi Raikkonen and Ferrari's Fernando Alonso start eighth and ninth.
The notoriously capricious Spa climate had made merry with the pecking order in the first part of qualifying, with Caterham's Dutch driver Giedo van der Garde, who usually brings up the rear, ending up as third fastest.
Both Marussias, perennial back-markers, made it through to the second phase - with Max Chilton making the most of tricky conditions to claim the best qualifying result of his rookie season at 16th.
Both Williams and Toro Rosso drivers, including Australian Daniel Ricciardo, who is tipped to graduate to Red Bull next season, missed the cut.
With rain forecast for today, the race is up for the grabs, as Vettel recognised. "A shame to miss pole again, but I'm quite happy. All in all a good day for the team," he said. "We expect similar conditions - rain, dry, a bit of everything, so we'll see."