The world champion had to park in the garage after just three laps at the start of the afternoon when the team detected the water system fault.
Vettel would not reappear for almost an hour, but when he did, he left his rivals in no doubt whatsoever about his pace this weekend as a 1m37.718s lap on his second medium-tyre run put him 0.757 seconds clear of the pack.
Even during Vettel's absence, Red Bull had been in front for most of the session thanks to Mark Webber.
The Australian had produced a 1m39.485s on hard tyres just after the half-hour mark to depose early pacesetter Nico Rosberg's Mercedes, and then found another two tenths next time round.
Felipe Massa enjoyed a seven-minute spell in first place when he delivered a 1m39.106s, but soon after Webber switched to the softer Pirellis and regained the top spot.
Webber's first medium-tyre effort was a 1m38.958s, and he swiftly improved to 1m38.475s - although that was firmly eclipsed by Vettel's pace when the German was back in action.
There was some cause for optimism for Vettel's title rival Fernando Alonso's Ferrari team. Alonso took third, just 0.008s down on Webber, and Massa had at least ended up quickest in the 'hard tyre' segment of the session.
The McLarens completed the top five, Lewis Hamilton escaping a Turn 13 spin to pip team-mate Jenson Button.
Sometime pacesetters Massa and Rosberg ended up sixth and seventh.
Bruno Senna was the top Williams driver in eighth, while his team-mate Pastor Maldonado suffered an apparent engine problem in the closing seconds.
Kamui Kobayashi lost a lot of track time to an exhaust problem before taking his Sauber to ninth ahead of Michael Schumacher's Mercedes.
The Lotus duo were just outside the top 10. Romain Grosjean tested the limits of the dramatic Turn 1 with a quick spin late on, emulating an earlier error by Caterham driver Vitaly Petrov.
The other Caterham also had an incident. Heikki Kovalainen had to nurse his car around a full lap with a puncture following a light brush with Jean-Eric Vergne's Toro Rosso, which sustained front wing damage in the tangle.
At the tail of the field, the troubled HRT team did not leave the garage for the first half of the session and completed significantly less mileage than most of the pack.