Michael Schumacher was third with sole title rival Kimi Raikkonen fifth quickest.
The Italian grabbed the third pole position of his career, knocking Honda's Jenson Button off the top spot as the seconds ticked away at the end of the session.
Electrical gremlins held up Lewis Hamilton in Italian Grand Prix practice on Friday after the Mercedes driver had lapped more than half a second quicker than anyone else in the morning session.
The Formula One season winds up in Abu Dhabi on Sunday with both titles won, Lewis Hamilton aiming to close the year on a winning note and big money still at stake for those further down the paddock pecking order.
Variously described as F1's first black or Anglo-Caribbean driver, his debut is probably the most eagerly-awaited of any in recent years.
Former champions Williams, newcomers Spyker, tail-enders Super Aguri and Toro Rosso are at loggerheads over cars that have yet to see the light of day.
The McLaren driver was crowned driver of the year by Britain's Autosport magazine despite being beaten to the F1 title by Alonso.
Lewis Hamilton landed an early psychological blow ahead of Formula One's Abu Dhabi title showdown by lapping faster than Mercedes teammate Nico Rosberg in both Friday practice sessions.
The decision confirmed Germany's Nick Heidfeld as the eighth placed driver and relegated Ralf Schumacher to 11th at the San Marino Grand Prix.
Ross Brawn said the memory of Nigel Mansell's failure to win the 1986 title from a similar position still lingers.
Felipe Massa said farewell to thousands of Ferrari fans in Italy on Sunday and received a trophy nearly as tall as him to celebrate his time with the Formula One team.
The two drivers are vying for a place alongside Australian Mark Webber at BMW-Williams for next season.
Sebastian Vettel drove a flawless tactical race to claim his maiden victory for Ferrari at the Malaysian Grand Prix on Sunday, registering the first Formula One win for the Italian team since 2013.
Launching a scathing attack over his fellow drivers for not presenting a united front on the introduction of Halo device, Ferrari's Sebastian Vettel has favoured the launch of head protection device for the 2017 Formula One season saying nothing could 'justify death'.
World champion Michael Schumacher was only 15th fastest in free practice for the Spanish Grand Prix.\n\n
BAR said they took the decision to take up the option on Button's contract on July 20 and informed the driver's management team.
The Swiss-born racer, who gave Williams their first grand prix victory at Silverstone in 1979 and won four races for Ferrari, was 67.
Lewis Hamilton and Sebastian Vettel battle to match the late Argentine's 1950s feat of five world championships.
Although Ralf Schumacher, last year's pole-setter in a Williams, qualified second fastest the German lost 10 places on the grid after having an engine replaced on Thursday.
Germany's Nick Heidfeld was second for Williams with Australian team mate Mark Webber third for his first podium finish.
Formula One world champion Lewis Hamilton set the pace in an incident-filled opening Monaco Grand Prix practice on Thursday, with debris and a loose drain cover bringing an early end to the session.
Lewis Hamilton took a huge stride towards a fourth Formula One title on Sunday with victory in an incident-packed Singapore Grand Prix after Ferrari title rival Sebastian Vettel crashed out at the start.
The Colombian has promised Williams he will do all he can to help them win the constructors' title.
Michael Schumacher may be still two races away from a record sixth F1 title, but according to his team's web site he has already won it.
Williams hopeful Nick Heidfeld was fastest at the start of what could be a decisive five-day test programme with the Formula One team in southern Spain on Monday.
"It was unbelievable, to have a fastest race lap under normal conditions in your first ever Grand Prix," Nico Rosberg's father, 1982 champion Keke said.
Ralf Schumacher eclipsed his older brother Michael in Friday's first qualifying at the German Grand Prix.\n\n
