Ferrari's decision to begin Q3 on intermediate tyres instead of supersofts backfired spectacularly as the rain they expected held off just long enough for Hamilton to set a fastest lap of one minute, 27.760 seconds - three-tenths quicker than teammate Valtteri Bottas.
Vettel trails his fellow four-times champion by 50 points in the standings with just four races left after Japan.
Haas driver Kevin Magnussen was 12th fastest, having used softs on his first run and lapping 0.548s slower than Grosjean in Q2 on the same compound.
The Haas eventually shed the damaged tyre, and bodywork that splintered thanks to the flailing rubber, and the safety vehicle was deployed while the debris was cleared. "But the gap was there - I had more speed, I would have made the corner".
Both were forced to abort their runs to take on slicks, meaning their first flying laps came just as rain was on the cusp of falling, and while Raikkonen was able to post a 1m29.521s to secure fourth behind Red Bull driver Max Verstappen, Vettel ran off the track at Spoon Curve after the rear stepped out and posted only a 1m32.192s.
The Dutchman served a five-second time penalty for leaving the track and not returning safely, forcing Raikkonen onto the grass after overrunning a chicane.
Perez, however, had his opportunity to pass when Leclerc triggered a virtual safety vehicle on lap 41.
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"Keep him [Bottas] under pressure, keep it clean".
The former Ferrari diver is a popular member inside the paddock, especially with Red Bull's Daniel Ricciardo as the duo exchanged a friendly hug on the grid in the moments leading up to the race.
Tactical errors have seen Ferrari pit too early, too late, fit the wrong tires; but Vettel has been equally at fault for throwing away the championship.
Honda disappointment: After qualifying sixth and seventh there was a real buzz around Toro Rosso-Honda ahead of the start of the race.
Driver of the day Tricky one, this. I remember Austria this year where we pitted Lewis out of the lead, so I think we are trying to stay humble and accepting that it's not always easy. Hamilton was supreme, driving superbly and overshadowing Bottas in what has become in recent races a dominant auto. Fernando Alonso drove well to pressure faster cars in the bad McLaren. He's going to do it soon.
The Briton, victor of five of the last six races had always been favourite for pole having dominated practice but Vettel had looked competitive until the botched tyre choice.
"We've gone from strength to strength as a team this year".
In the first instance, Verstappen was given a 5-second time penalty and a single penalty point on his license as the stewards had ruled that he had "cut the chicane and rejoined track on the racing line in turn 17 and in the process collided with vehicle 7".