The Australian's one minute 22.693 seconds lap time was set on soft-compound Pirelli tyres with just seven minutes of running remaining and put him 1.655 seconds clear of Lewis Hamilton's Mercedes.
After the late-morning rain left drivers with a wet track to tackle, rain tyres were the weapons of choice during the early afternoon running, with Webber recording a series of 1:44 laps.
Track conditions soon improved enough for intermediates, with Paul di Resta the first man to try the green-stickered Pirellis in his Force India.
Webber having lowered the pace to the 1m38s bracket, it was Felipe Massa who was the first to gamble on a switch to slicks, the Ferrari driver using medium-compound rubber to gradually bring the times down into the 1m30s.
By that stage conditions were dry enough to allow a range of tyre strategies to be deployed, with medium, soft and supersoft rubber all being used at various points during the afternoon.
A late red flag, caused when Massa's Ferrari stopped at the exit of Turn 9, led to a flurry of fast times during the 12 minutes that remained.
Webber and Hamilton initially exchanged the top spot before the Red Bull driver twice went quicker still to end the day on top.
Hamilton, who suffered a quick spin at Turn 1 while on pushing hard on slicks, was followed by Jean-Eric Vergne's Toro Rosso, the Williams of Valtteri Bottas and McLaren's Sergio Perez.
Hamilton completed more laps than anybody else. His total of 113 was one more than Massa. Perez was the only other driver to get into triple figures.
Pos Driver Team Time Gap Laps
1. Mark Webber Red Bull 1m22.693s 90
2. Lewis Hamilton Mercedes 1m24.348s + 1.655s 113
3. Jean-Eric Vergne Toro Rosso 1m25.017s + 2.324s 59
4. Valtteri Bottas Williams 1m26.458s + 3.765s 85
5. Sergio Perez McLaren 1m26.538s + 3.845s 100
6. Esteban Gutierrez Sauber 1m26.574s + 3.881s 92
7. Paul di Resta Force India 1m27.107s + 4.414s 57
8. Felipe Massa Ferrari 1m27.541s + 4.848s 112
9. Max Chilton Marussia 1m28.166s + 5.473s 78
10. Charles Pic Caterham 1m28.644s + 5.951s 83
11. Romain Grosjean Lotus 1m34.928s + 12.235s 52
- Motor Racing
- Sports & Recreation
- Lewis Hamilton
- Felipe Massa