Ferrari have tended to be quicker off the line than Mercedes in recent races, a divergence which was a factor in the crashes between Sebastian Vettel and Valtteri Bottas in France and then Hamilton and Raikkonen at Silverstone.
"Ferrari have been quickest all weekend and we were doing our best to catch up, but then the heavens opened and it was fair game".
In the final bout of qualifying simulations Bottas briefly went fastest on a 1m16.229s, at nearly exactly the same time as Hamilton spun at the chicane.
"In wet conditions we are not as confident as in the dry so there is some work to do and I think today it was a tricky session and it could have been anything".
"I don't think there was an bad lot missing, but we weren't quick enough", he explained.
Lewis Hamilton won his second race in a row
The German, who will start alongside team-mate Raikkonen from the second row, told Sky F1: "In the dry we were under control. I think we managed it well until the end, we were missing a bit but that's how it is".
Championship leader Lewis Hamilton was fourth in the second Mercedes behind the two Finns, but ahead of the two Red Bulls of Daniel Ricciardo and Max Verstappen. "Tomorrow I will have a fight on my hands", said Ricciardo. With both Hamilton and Bottas pitting for the second set of wets, the W09s were significantly faster over the Ferraris, turning the qualifying into a battle between Hamilton and Bottas.
Qualifying follows later on Saturday with the Hungarian Grand Prix, the last before a four-week mid-season break, taking place on Sunday.
Hamilton will now be favorite, providing he makes a clean getaway without incident, at a circuit where overtaking has always been hard.
Frenchman Esteban Ocon qualified 18th with Mexican Sergio Perez, whose legal claim for millions owed triggered the administration, was 19th.