Vettel set a time of 1m52.522s on the wet track, edging his teammate by 0.109s. Both drivers completed just six laps.
A damp wind was blowing from the track making conditions tricky at best with a number of drivers spinning off.
Lewis Hamilton was provisionally half a second quicker than Vettel before running off-track at Stowe and heading immediately to the garage.
Lotus drivers Pastor Maldonado and Romain Grosjean were third and fourth fastest. Grosjean spun at the exit of Club and nearly hit the pit wall.
Adrian Sutil was fifth quickest, setting his best lap on intermediate tires just before the end of the session.
Teams did limited running because of the wet conditions at Silverstone, and Mercedes drivers Lewis Hamilton and Nico Rosberg did not set lap times, even though they were fastest in the first and second sectors.
Mercedes co-team boss Toto Wolff said: "It's not perfect with these conditions but it does not make a lot of sense to run at the moment. You need to save tires."
Ferrari’s Fernando Alonso also chose not to set a time, while his teammate Kimi Raikkonen finished 10th.
|1.||Sebastian Vettel||Red Bull-Renault||1m52.522s||+0.000s||6|
|2.||Daniel Ricciardo||Red Bull-Renault||1m52.631s||+0.109s||6|
|6.||Daniil Kvyat||Toro Rosso-Renault||1m53.654s||+1.132s||15|
|11.||Jean-Eric Vergne||Toro Rosso-Renault||1m54.602s||+2.080s||6|
|12.||Esteban Gutierrez Sauber-Ferrari||1m54.761s||+2.239s||13|
|14.||Nico Hulkenberg||Force India-Mercedes 1m55.688s||+3.166s||6|
|15.||Sergio Perez||Force India-Mercedes 1m56.918s||+4.396s||7|
|19.||Max Chilton||Marussia-Ferrari||No Time||No Time||1|
|20.||Fernando Alonso||Ferrari||No Time||No Time||4|
|21.||Nico Rosberg||Mercedes||No Time||No Time||4|
|22.||Lewis Hamilton||Mercedes||No Time||No Time||5|