Raikkonen, who won the season-opening Australian GP and lay second behind Vettel in the drivers' championship, was 0.03 seconds faster than Webber and 0.12 quicker than Vettel.
Ferrari's Fernando Alonso was fourth while his teammate Felipe Massa, who topped the charts in the first practice, settled for sixth.
Force India's Paul di Resta was a surprising fifth.
Several drivers had trouble with the hot and dry conditions, including Mercedes' Lewis Hamilton, who finished 10th, and McLaren's Jenson Button, who came in 11th - the latest setback for a team that has struggled to be competitive.
The session was largely uneventful, except for Sauber's Esteban Gutierrez clipping his tire on the wing of Caterham's Charles Pic, forcing the Mexican back to the pits. Gutierrez has been slow to adjust to F1 and was penalized five grid places for the Bahrain race, after he was blamed for a collision with Force India's Adrian Sutil in China.
The race has been overshadowed to some degree by the political crisis in the divided Gulf country.
While the circuit has been quiet, daily clashes have taken place in nearby Shiite villages between pro-democracy protesters and riot police. Hardline protesters hope to embarrass the ruling royal family with increased violence, while more moderate protesters, who support the race, merely want to highlight their demands for a greater voice in the country.
Rights groups, meanwhile, have condemned the race going ahead amid allegations of crackdowns and widespread arrest of government opponents.
Teams and drivers have mostly remained silent on the political crisis, and the FIA, the governing body of world motor sports, has endorsed the race. It said the Bahrain GP should proceed "following assurances from the local promoter and the authorities that security, their responsibility, will be guaranteed for all participants."
"The FIA and FOM also strongly believe that sport can often be a force for good and that the staging of the grand prix in Bahrain will come some way in helping soothe some of the issues which have been raised in the media," the FIA said in a statement.
Formula One Boss Bernie Eccelstone scoffed at reports of trouble, telling reporters "you guys are the ones who write about the rubbish. Have you found any?"
"Looks all right, doesn't it?" he said. "I think anyone who really wants to see and talk about human rights should go to Syria, maybe. There are plenty of places in the world like Egypt where they got rid of dictators and put democracy in. Since then, there has been more trouble."