Michael Schumacher broke the record of late great Ayrton Senna by storming to his 66th pole position of his career
The Renault driver scored his second victory in three races to extend his lead in the Formula One world championship to 14 points.
Narain Karthikeyan finished 17th in Saturday's first qualifying for Sunday's Monaco Grand Prix.
Lewis Hamilton has admitted he wants to see out his career with McLaren.
Alonso's victory at Ferrari's home circuit was his third win in a row this season and the team's fourth in four races.
Team by team analysis of Sunday's San Marino Formula One Grand Prix (listed in championship order).\n
He will start on the front row alongside Renault's Fernando Alonso. India's Narain Karthikeyan qualified on 17th place.
With Schumacher departed, Alonso will be the only champion in Formula One next season but he joins a team that has not won since 2005.
Michael Schumacher was left with a mountain to climb in the last race of his Formula One career after qualifying 10th for the title-deciding Brazilian Grand Prix.
Schumacher, retiring after Sunday's race at the Interlagos circuit, was sixth fastest with a lap of one minute 13.713 seconds in the afternoon session despite a spin off on to the grass.
"Don't ever write that guy off. It's not over until it's over," said former F1 champion Damon Hill.
Fernando Alonso hailed his surprise Japanese Grand Prix victory as a gift from God.
Michael Schumacher fans were crushed when his engine and title hopes went up in smoke.
The Renault team boss said they have done everything they could to support Fernando Alonso
Michael Schumacher was the slowest driver to complete a lap, behind even the two Minardis and 27.4 seconds slower than Fisichella.
Optimism and tributes to Michael Schumacher on the Rediff F1 Chat following the Italian Grand Prix.
The Finn pipped the seven times champion by just 0.002 seconds.
Should Michael Schumacher stay or should he go? What's your verdict?
McLaren rookie Lewis Hamilton drew praise from Formula One's most successful driver, seven times champion Michael Schumacher, on Friday.
The main suspense concerns the future of Michael Schumacher, who could announce his retirement.
The six-times world champion said racing has become easier now without any worries about records.
Michael Schumacher is confident he can overtake Fernando Alonso with four races to go in the F1 season.
Jacques Villeneuve slammed Michael Schumacher for his on-track conduct over the years.
The Formula One champion broke the lap record in practice for the season-opening Australian Grand Prix.