WebberÃ¢â‚¬â„¢s team-mate Sebastian Vettel was third quickest between FerrariÃ¢â‚¬â„¢s Fernando Alonso and Felipe Massa who recovered from a disappointing first session.
By contrast, rivals McLaren slipped back as Lewis Hamilton and Jenson Button were eighth and thirteenth respectively as they tested their new upgrades which arrived at the eleventh hour.
Once WebberÃ¢â‚¬â„¢s fastest lap had been achieved, most of the teams went into test mode rather than throwing it around the new circuit.
Webber completed just 15 laps, the second fewest of any driver as he spent the closing stages of the race in the pits as his team worked to repair an electronics problem. Once again, Red Bull appear to have the pace, but have reliability problems hanging over them.
Crosswinds continued to hamper all drivers heading into the infield section, with a few more off-track excursions following this morningÃ¢â‚¬â„¢s adventures.
Red Bull have been consistently quick in the first two practice sessions, but they look fragile ahead of the race. McLaren meanwhile will have to pour over the technical data from the first two sessions and decide whether to run their new upgrades.
With tweaks made to their cars between practice one and two the cars were slower in the second session. How much of that is down to strategy and testing ahead of the race, however, is unclear.
Mercedes finally showed some promise as Nico Rosberg lapped less than a tenth slower than Massa, with team mate Michael Schumacher half a second slower to take sixth.
Surprisingly, Vitaly Petrov outpaced team-mate Robert Kubica with the under-pressure Russian taking seventh, just ahead of Hamilton and Force IndiaÃ¢â‚¬â„¢s Adrian Sutil.
Rubens Barrichello lapped a time of 1:32:967 to round out the top 10 with 1.7 seconds separating the drivers.
LotusÃ¢â‚¬â„¢ Jarno Trulli completed just three laps as a mechanical problem kept the Italian in the pits for much of the session, his quickest time a very slow 1:42:901.
His team mate Heikki Kovalainen showed the Lotus has some pace to again easily beat the other rookie teams, but was eight tenths slower than 18th placed Jaime Alguersauri in the Toro Rosso.
Sakon Yamamoto, in for Bruno Senna at Hispania, continued to be way off the pace as he came in 1.3 seconds slower than team mate Karun Chandhok, and seven seconds slower than Webber.
TomorrowÃ¢â‚¬â„¢s final practice will give an indication of how the upgrades have worked, and more of an idea about what we can expect in qualifying.
Final practice begins on Saturday at 10:00 BST before qualifying at 13:00.
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