Many of the teams utilised the final hour of free practice to fine-tune the set-up of their cars ahead of the tricky prospect of qualifying on a much cooler track later on Saturday.
But it was world champion Vettel who stormed to the top of the time sheets once more as everyone had a blast of just under 10 minutes on the softer tyre.
Vettel's time of one minute and 41.349secs was marginally slower than his best effort on Friday but was still quick enough to see him outpace Red Bull partner Webber by just over two tenths of a second.
The Mercedes of Lewis Hamilton appeared to be the best of the rest as the Brit once again finished the session with a time only bettered by the Red Bull duo, while his team-mate Nico Rosberg was a place further back.
Romain Grosjean set the fastest time in first practice before a break disc failure ruined his second session, but the Frenchman recorded another competitive time on Saturday to sit fifth.
His unsettled, and reportedly unpaid, team-mate Kimi Raikkonen was down in ninth, with the McLaren of Jenson Button and the Sauber pair of Nico Hulkenberg and Esteban Gutierrez separating the two Lotus cars.
Jean-Eric Verne rounded out the top 10 with the Torro Rosso driver outpacing team-mate and Red Bull-bound Daniel Ricciardo, who was down in 15th.
Ferrari are battling with Mercedes for second place in the constructors' championship but their fight to overhaul their German rivals seems to be stuttering as both Fernando Alonso and Felipe Massa struggle for pace at the Yas Marina circuit.
Alonso could only manage the 11th-fastest time whilst Massa was 14th with the Force India of Paul Di Resta and Williams' Valtteri Bottas in between.
Pastor Maldonado was 16th in the sister Williams and Adrian Sutil, who was complaining throughout the first half of the session that he was suffering from both understeer and oversteer inside his Force India, ended down in 17th.
The second McLaren of Sergio Perez was 18th as the Mexican did not set a fast time until towards the end of the session after a prolonged period in the garage.
Caterham's Giedo van der Garde and Charles Pic were 19th and 20th respectively while Max Chilton finished ahead of his Marussia team-mate Jules Bianchi who was slowest after a big shunt into the barrier caused damage to his car.