Hamilton denied Red Bull a one-two by squeezing in between Webber and his third-placed team-mate Sebastian Vettel.
The first half of the session, when the field was still working with medium tyres, saw the Red Bulls leading the way for a spell early on, before Raikkonen went in front for Lotus and then Hamilton got in a 1m21.706s to put himself over half a second clear of the field just before the midway point.
Hamilton squeezed that lap in just before the soft tyre times started to flow, with Vettel lapping in 1m21.671s to go quickest. He stayed there until team-mate Webber edged ahead by 0.121s five minutes later.
Unusually for a Saturday morning, that time stood until the end, with the only major late change being Hamilton's appearance in second place.
Bruno Senna suggested his promising Friday afternoon performance was no fluke by taking a very strong fourth for Williams.
Ferrari took its time joining the fray, then sealed fifth and eighth with Fernando Alonso and Felipe Massa. The pair sandwiched the two Lotus drivers, Raikkonen and Romain Grosjean taking sixth and seventh.
Paul di Resta was ninth for Force India, with Jenson Button rounding out the top 10 in the second McLaren.