In tricky conditions at the Spa-Francorchamps circuit it was nip and tuck between the main championship contenders, with Rosberg grabbing bragging rights at least going into the race.
Rosberg captured the 11th pole of his career by a quarter of a second from Hamilton, who again made slight mistakes in the final session.
But after starting 20th and from the pit lane in the last two races following a brake failure in Germany and car fire in Hungary, the 29-year-old will likely be relieved to simply have come through the session unscathed.
In seven previous attempts Rosberg had failed to even qualify in the top three at Spa, but, given Mercedes’ dominance this year, that record was always going to be broken.
In total for Mercedes it is now 11 poles from 12 grands prix this season, with Rosberg clinching seven of those to Hamilton’s four.
Pole on this track, however, matters little given its nature as it is wide with numerous overtaking places, and the fact it is also seven kilometres long.
For Rosberg, who has never previously been on the podium here, he was naturally happy enough to finish ahead of Hamilton.
“To get pole is awesome,” Rosberg said.
“At this track, which is one of the most special of the year, to be in front here is great
“It wasn’t quite so difficult out there as it looked as the conditions always meant we were on intermediate tyres.
“After some fine-tuning with my engineers we got there in the end, but it’s only qualifying. There’s a long race tomorrow, although overall I’m happy.”
Hamilton revealed a technical issue hampered his hopes of pole as he said: “I had a glazed front-left brake.
“That meant the car was pulling to the right, and I couldn’t get rid of that, so I was losing massive amounts (of time).”
For Hamilton, it is his highest grid position for five races since Canada in June.
He added: “I’m just happy to be here. A great feeling.”
Behind the Mercedes duo, Red Bull’s Sebastian Vettel was the nearest challenger, albeit finishing an astonishing 2.2secs adrift of Rosberg such is their power advantage
Vettel knew he could have done no more as the reigning four-times champion remarked: “It would be nice to be further up.
“But the gap is quite big, so it was the best we could do.
“It was tight behind the Mercedes, but it was a good challenge, and for sure I’m happy with third.”
Overall, it was a qualifying session spiced up by a torrential downpour 40 minutes prior to the start that even included a hailstorm, such is the capricious nature of the Ardennes that surrounds the track.
To add to the entertainment value of the weather, the sun managed to break through ahead of the opening session, but the earlier rain had guaranteed a wet circuit for the initial 18-minute run.
Further rain at the end of Q1 and throughout most of Q2 provided additional drama and uncertainty, whilst for the top-10 shoot-out the sun returned.
In the end Mercedes had no challenger, although behind the battle behind was intense, with Vettel narrowly ahead of Ferrari’s Fernando Alonso who starts fourth.
Red Bull’s Daniel Ricciardo starts fifth ahead of Williams’ Valtteri Bottas, who was expected to be closer, only for the conditions to hamper the Finn and team-mate Felipe Massa who starts ninth.
McLaren duo Kevin Magnussen and Jenson Button line up seventh and 10th, with Kimi Raikkonen in his Ferrari eighth.
Outside of the top 10 the Toro Rosso pair of Daniil Kvyat and Jean-Eric Vergne, being replaced next year by 16-year-old Max Verstappen, will occupy 11th and 12th on the grid.
Force India’s Sergio Perez lines up 13th ahead of Adrian Sutil in his Sauber, the Lotus of Romain Grosjean and Marussia’s Jules Bianchi, the latter producing a credible performance in a slower car.
At the end of Q1 Lotus’ Pastor Maldonado, who spun at the Bus Stop on a quick lap, and Nico Hulkenberg in his Force India were the primary casualties and will start 17th and 18th.
Marussia’s Max Chilton lines up 19th, but finished 1.5secs down on Bianchi, whilst behind the Briton will be Sauber’s Esteban Gutierrez, who suffered a technical failure midway the session through that halted his running.
On the back row will be the Caterhams, but credit to debutant Andre Lotterer.
The three-times Le Mans 24 Hours winner finished ahead of team-mate Marcus Ericsson, firmly underlining the Swede does not deserve his place in F1