The Red Bull driver, who has not won a race since last season when he wrapped up his fourth successive title, lapped the Silverstone circuit in a comparatively slow time of one minute 52.522 seconds.
Australian team mate Daniel Ricciardo, who has out-qualified Vettel in six of eight races so far, was second fastest.
"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 tyres," said Mercedes motorsport head Toto Wolff.
The two Mercedes were still fastest in the first two sectors and remain the clear favourites for Sunday's race.
Last year's race winner Rosberg leads Hamilton, who was quickest in Friday practice with a best lap of 1:34.508, by 29 points with 11 races remaining.
Saturday's qualifying was also expected to be wet.
- Sports & Recreation
- Motor Racing
- Nico Rosberg
- Lewis Hamilton
- Daniel Ricciardo
- Silverstone circuit
- Fernando Alonso