The Singapore Grand Prix takes place this weekend, where Button is currently in second position and Hamilton holds fourth place and McLaren-Mercedes is in second place.
"We're kind of boring, " said reserve Ronnie Brewer, who has often started in Hamilton's place.
When it resumed, Hamilton lost first place after a slow pit-stop with Alonso eventually appearing at the head of the field.
As the session drew to a close Massa briefly jumped above the 23-year-old, but a superb lap saw Hamilton regain his place at the top where he had looked set to finish for the second successive session.
Toyota's Jarno Trulli was delighted he could hold out Hamilton to claim fourth place.
Hamilton fell to sixth place, and as his contender -- Ferrari's Felipe Massa -- crossed the finish in first place, it looked as though the title had slipped through his grasp for the second year in a row.
Vettel could not find the pace required, while McLaren's soon-to-be deposed world champion Lewis Hamilton could manage only 18th place.
World champion Lewis Hamilton will start from 18th place, one behind McLaren teammate Heikki Kovalainen, as both failed to make it past the first hurdle.
CNN: Barrichello wins pole as Button blows it in rain-lashed Brazil
Hamilton had been awarded third place in Melbourne before being stripped of his points after he and Ryan were adjudged to have given stewards "deliberately misleading" evidence in a post-race hearing on Sunday.
Meanwhile, McLaren's Lewis Hamilton has had a five-place grid penalty imposed for Sunday's race in Shanghai due to a change of gearbox.
Amazingly, Hamilton still managed to secure his place in the top 16 without reaching the quarter-finals of a ranking event in the 1997-98 season.
The six points claimed by Hamilton also took McLaren into first place in the constructors' championship with Massa's Ferrari team-mate Kimi Raikkonen carelessly colliding with the wall while in fifth place.
Alonso, who had the good fortune to come in for an early pit stop before the accident involving his Renault team-mate Piquet, drove peerlessly away after the second safety car delay, with Hamilton content to settle for third place.
McLaren were found guilty of misleading race stewards following the Australian Grand Prix, which led to Lewis Hamilton - who had been awarded third place - being disqualified from the race and stripped of his points.
The Brazilian drove so brilliantly and Hamilton had somehow managed to end up in sixth place with one corner to go - but, well, you know what happened next.
Kovalainen drove alongside Lewis Hamilton for McLaren in 2008 and 2009, but his place this year has been taken by reigning world champion Jenson Button.
However, Alonso had other ideas and improved from his seventh place in first practice to finish ahead of Hamilton and set the third fastest time of the day.
"It's a very demanding circuit, the kind of place that punishes any mistakes hard, " stated Hamilton.
In one final twist, however, Hamilton overtook Glock's slowing Toyota to clinch the fifth place he needed - and with it the title.
Alonso ended with the fastest time but was later handed a five-place grid penalty -- with eventual race winner Hamilton elevated to pole position.
Starting on pole, Alonso protected his lead even after a pit stop on lap 16 but the hard tires on Lewis Hamilton's McLaren car set up a tussle for first place on lap 19.
With five minutes of the first-half left, Charlie Mulgrew stepped up to place one of his trademark free-kicks and Hamilton keeper Tomas Cerny was at full stretch to parry the ball out for a corner.
BBC: Hamilton's David Elebert (left) tussles with Sone Aluko
Ferrari's world champion Kimi Raikkonen, three points behind Hamilton in this year's title race, took third place in the grid with one minute 18.735 seconds while Fernando Alonso of Renault will start the race alongside the Finn in fourth.
If the race finishes as it starts then third place will be enough for McLaren's Lewis Hamilton to hang on to his lead in the title race (124 pts) from the two Red Bulls of Mark Webber (121 pts) and pole-sitter Sebastian Vettel (115pts).
Mr. ANTHONY HAMILTON (Musician): There's a proper time and place for everything, and once you put so much time into it, you'd be a fool to turn around and walk away from it, 'cause I tasted it.
Massa's team-mate Raikkonen, who crashed out of second place shortly after losing the lead, is 19 points behind Hamilton.
The win puts St Johnstone in joint sixth place in the Scottish Premier League alongside Dundee United, while Hamilton have yet to record a win at home all season.
Late-race rainfall had unpicked Hamilton's best-laid plans to cruise home in the fifth place he needed to deny Massa the crown and it looked like he would blow his chances of becoming champion for the second season running.
"I think finishing in this place, it will be a tough race for sure, " said Hamilton.
The McLarens of Jenson Button and Lewis Hamilton will make up the third row of the grid, with Button in fifth place.
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