Kimi Raikkonen rediscovered his mojo, leaping from fourth on the grid to first by the end of lap two, capitalizing on a spin from polesitter Hamilton on a damp track.
Hamilton closed right up to Raikkonen on lap 42 but he fatefully cut the Bus Stop chicane after pulling out of a passing move at the end of the lap.
Junqueira knocked Da Matta off the top spot just one minute from the end with a lap of 1:42.151 at 142.659 mph (229.538 kph).
The prospect of Hamilton winning the title, however, was simply too good to ignore so, thanks to some creative thinking, we found a hotel room that offered a view of the pit straight and the corners at the end of the lap.
Anstey had increased his lead by another four seconds by the end of the third lap.
BBC: Anstey pushes his bike to the limit around the TT course
Adrian Archibald retired at the end of the first lap while Guy Martin and Ryan Farquhar ran out of fuel on lap two.
BBC: Anstey pushes his bike to the limit around the TT course
Franchitti's Honda-powered Lola pulled away to a 2.6-second lead at the end of the first lap and he cruised to the eighth win of his career.
Raikkonen is caught out during the twisty finish to the lap to end up in third while Alonso struggles on the harder tyres during his last-gasp effort to end up in fourth.
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By the end of the first lap he was already two seconds up on the leading time and went on to clock a series of sub-30 seconds laps as he moved with grace and power across the ice.
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Manchester United's victory lap through the end of the season began Sunday with a 1-1 draw at Arsenal that once again shook up the race for the last two Champions League qualification spots.
Reigning world champion Sebastian Vettel also adopted the same tire strategy but didn't complete a timed lap in Q3 to end up one place behind Button in ninth.
"Six laps from the end I asked about the tyre situation and about the weather conditions, and I said every time I'll stay out, 'one more lap, one more lap' and at the end I stayed out for the whole race, " the German told BBC Radio 5 Live.
As the chequered flag was waved to end qualifying for Sunday's 60-lap race on the 6.513km road course, both of the drivers were near the back of the track, pushing for a final quick plap.
Toseland, who enjoyed his best performance of last season at this circuit, was among the pacesetters over the opening laps and ended up seventh fastest despite his misdemeanour - merely a result of pushing the front end too hard as he chased an improved lap time.
And his race came to a premature end when he spun on the final corner of lap 23.
BBC: SPORT | Motorsport | Formula One | Webber rues mistakes
Those who made it to the end survived multiple accidents, including one on the second lap, and 10 caution flags.
"At the end that was as far as I could get out my lap, " said Hamilton, who actually did a lap in the second qualifying session that would have put him on pole had he repeated it.
BBC: Sebastian Vettel beats Lewis Hamilton to Abu Dhabi pole
Britton deliberately slowed down with one lap left after believing the race was coming to an end.
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