Lewis Hamilton produced a great lap to stick the Mercedes on pole.
The Australian, fourth fastest in Friday's rain-hit morning session, produced a brilliant lap in the afternoon session at Silverstone.
Williams had looked set to take the second row, but Vettel produced a spectacular lap to take third in the under-powered Red Bull-Renault.
And Chris O'Hare took 1500m bronze behind the controversial Mahiedine Mekhissi-Benabbab, who produced a last lap of 52.17 to destroy the field after a slow opening 800m.
Tyco Suzuki rider Martin produced a fastest lap of 115.083 mph which left him well ahead of Milwaukee Yamaha man William Dunlop (113.901).
William Dunlop edged out his brother Michael in the first Supersport qualifying session for the Ulster Grand Prix. William produced a fastest lap of 115.161 which left him just ahead of Michael (115.135).
Seeley, after struggling in qualifying, was in the second group of riders in the opening Supersport race but produced a last-lap charge to grab first place on corrected times by 1.3 seconds.
Seeley produced a brilliant last lap to snatch victory over Michael Dunlop in Thursday's opening Supersport race.
Toomebridge rider Laverty produced a superb final lap overtake on Marco Melandri to win the opener while Sykes won the title by finishing third.
Johnson, 33, led from the start, although Anstey produced a brilliant final lap to reduce the margin from four seconds to only 0.1 at one stage.
