The Flying Finn was clipped by Christian Klien's Red Bull and spun off the track
Kimi Raikkonen, the only man standing between 24-year-old Alonso and the title, made an error in qualifying for the Brazilian Grand Prix. and starts on the third row in fifth place.
McLaren set the pace in Friday's Brazilian Grand Prix practice with Colombian Juan Pablo Montoya the fastest race driver.
Lewis Hamilton boosted his morale with the fastest lap in Russian Grand Prix practice on Friday after Mercedes team mate Nico Rosberg set the early pace and Ferrari suffered reliability problems.
Kimi Raikkonen went further, saying he had no intention of leaving McLaren.
India's Narain Karthikeyan will start 19th on the grid on Sunday's Turkish Grand Prix.
Fernando Alonso feels Sunday's inaugural Turkish Grand Prix could play to Renault's strengths.
The Finn, second in the Formula One championship to Renault's Fernando Alonso, suffered a blown engine in Friday's first free practice.
Ferrari's Michael Schumacher and Rubens Barrichello finished second and third respectively.
Germany's Nick Heidfeld was second for Williams with Australian team mate Mark Webber third for his first podium finish.
The Brazilian lapped 0.151s quicker than team mate Michael Schumacher in free testing at the Italian Grand Prix.
The German, winner of the season's first two races, had been second before coming in for a fresh set of tyres while Hamilton won with one stop from pole position.
The win also set a record, one that Hamilton had previously shared with seven times champion Michael Schumacher, of 41 wins from pole position.
The final three races will decide whether Ferrari's Michael Schumacher, Williams' Colombian Juan Pablo Montoya or Raikkonen takes the F1 title.
Renault's championship leader Fernando Alonso was pushed off the front row for his home Spanish Grand Prix.
The Finn fought back from sixth quickest in Friday's first practice session to edge out Schumacher for the fastest time overall.
The time sheet for Sunday's Malaysian Formula One Grand Prix.
Narain Karthikeyan finished 17th in the first qualifying round at the San Marino Grand Prix
Finland's Valtteri Bottas took his first Formula One pole position at the Bahrain Grand Prix on Saturday with a sizzling lap that ended Mercedes team mate Lewis Hamilton's bid for a seventh in a row.
"The reality check is a race weekend so there is nowhere to hide from that," said the Scot.
McLaren's Kimi Raikkonen is fully fit for Sunday's Italian Grand Prix after missing testing last week to recover from a crash at the previous race in Turkey.
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