Webber produced a superb lap at the end of qualifying to snatch pole from team-mate Sebastian Vettel, as the German looks to try and take over the lead of the championship from Fernando Alonso.
Webber's ability to bounce back from an engine mapping issue during final practice stunned Vettel - and secured the 200th pole for a Renault engine - who had been fastest during the first two parts of qualifying.
Hamilton, 38 points behind Vettel and a further four back of Alonso, was third-fastest as he recovered strongly after a difficult Friday.
But the 2008 champion needs to start eating into the points deficit with just five races remaining, and any factor that could limit Vettel's points haul here would be gratefully received.
And Webber's pole lap has the potential to make life awkward for Red Bull.
While Webber is 60 points back of Alonso, and 56 behind Vettel, he will not enjoy the prospect of relinquishing a lead to his team-mate regardless of the championship situation.
Indeed, earlier this weekend the Australian brushed off questions over whether he would help his colleague, simply stating: "I need to win".
The pair's relationship has been strained, particularly following their collision in Turkey in 2010 and a row over front-wing parts at Silverstone later that year which led Webber to describe himself as the "number two driver" within the team.
When Whitmarsh, who knows a no holds barred duel between the pair could play into Hamilton's hands, was asked about the prospect of Webber moving aside to allow Vettel to clear off and win, he thought it was unlikely.
"I don't think he will willingly, it is possible but I don't think he will," he said.
Hamilton, meanwhile, is hopeful the extended DRS zone between turns two and three will help his cause of trying to compete with the Red Bulls.
"Traffic has ben difficult just in practice and qualifying," he said. "But last year here it was very difficult for Mark to get past me and he was generally quite a bit quicker.
"But they have extended the DRS zone by 200 metres and so perhaps that will enable people to get closer and challenge. I hope there is more overtaking."
He added: "I want to beat Sebastian, I want to beat Fernando and I want to close that gap up, but they are so fast this weekend.
"There are 125 points left and I want to pick up as much as I can at each opportunity I have."
While Hamilton will start from the second row, his team-mate Jenson Button had a day to forget and ended up 11th.
Button was caught out by yellow flags when the Toro Rosso of Daniel Ricciardo ground to a halt in the final sector in the final moments of Q2.
That left Button unable to improve and he was bumped out of the top 10.
That leaves the Briton facing some tricky strategy decisions ahead of Sunday's race, but he has ruled out trying a one-stop approach, despite Pirelli believing it is a possibility.
"We were pretty much the quickest over a 13-lap stint yesterday so I think we have a good understanding of what the tyre can do and we will be doing a lot of laps on the prime tyre if it's a one-stop race," he said.
"Maybe it is possible but I will be surprised if people try a one stop tomorrow [Sunday]. I would love the chance to do a one-stop tomorrow but I do not think it is possible."