Robert Kubica took second for Renault, ahead of the Ferraris of Felipe Massa and Fernando Alonso.
Renault's Robert Kubica and Toro Rosso driver Jaime Alguersuari were handed reprimands for two separate incidents.
The 24-year-old was sixth in the morning and then seventh behind Renault's Robert Kubica in the afternoon.
Toro Rosso's Sebastien Buemi claimed sixth ahead of Williams' Nico Rosberg, with BMW Sauber's Robert Kubica eighth.
CNN: Barrichello wins pole as Button blows it in rain-lashed Brazil
Sebastian Vettel's Red Bull and Robert Kubica's BMW Sauber suffered engine problems on day one in Monte Carlo.
Renault's Robert Kubica and Mercedes' Nico Rosberg were next, ahead of Webber, Force India's Vitantonio Liuzzi and Alonso.
Removal of the two driver aids was weighing on a number of minds, including Heidfeld's team-mate Robert Kubica.
Australian GP runner-up Robert Kubica finished sixth in his Renault, ahead of current world championship leader Fernando Alonso.
Robert Kubica again impressed in his Renault, qualifying in seventh place with his team-mate Vitaly Petrov in 13th position.
BBC: Sebastian Vettel pips Fernando Alonso to German F1 pole
Red Bull's Mark Webber won the race with BMW's Robert Kubica finishing second.
Glock had been tipped as a potential team-mate for Robert Kubica at Renault.
The yellow safety flags came out after a collision between Red Bull's Sebastian Vettel and Robert Kubica in his BMW Sauber.
The McLaren driver clocked one minute 17.886 seconds to better Robert Kubica's mark for BMW Sauber by more than half a second.
Adrian Sutil was third fastest for Force India, followed by the BMW Sauber of Robert Kubica, Williams' Nico Rosberg and Rubens Barrichello (Honda).
The third man who entered the Chinese race in the championship reckoning, BMW Sauber's Robert Kubica, is out of the running after finishing sixth.
Polish driver Robert Kubica raced for the team in 2010, but missed all of last season following a rally crash in Italy in February.
Renault's Robert Kubica was fastest in the day's first practice session.
BBC: Lewis Hamilton fastest in Friday Australian GP practice
In Melbourne on Sunday, the safety car came out after a late collision between Red Bull's Sebastian Vettel and Robert Kubica in his BMW Sauber.
The other drivers to take part were Button's former Brawn teammate Rubens Barrichello in a Williams, Toro Rosso's Sebastien Buemi and Renault's new signing Robert Kubica.
He became the youngest driver to score a Formula One point when he replaced the injured Robert Kubica to finish eighth in the US Grand Prix in June.
The BMW Sauber team, who currently have Robert Kubica and Nick Heidfeld as their drivers, held a meeting on Tuesday where they made the decision to quit the sport.
Nick Heidfeld, who set the fastest lap in final practice, kept up his improved run of form to take fifth for BMW Sauber with team-mate Robert Kubica in eighth.
But after chasing the German closely through the first part of the race his hopes were ended when he came out from his pit stop behind Renault's Robert Kubica.
As part of the cascade of driver moves that will follow Alonso's switch, BMW Sauber's Robert Kubica is understood to have signed a contract to replace Alonso at Renault.
Renault, who will adopt the Lotus name next season, had hoped Polish driver Robert Kubica would be fit to resume action in 2012 having undergone arm surgery earlier this year.
But the McLaren man had to produce a dramatic last lap to pip Robert Kubica in the BMW who had surprisingly posted the quickest time moments before in Saturday's session.
McLaren's Heikki Kovalainen, who had finished second to Hamilton earlier in the day, was fourth in the afternoon, followed by the BMW Sauber of Robert Kubica and Toyota's Timo Glock.
Robert Kubica, Sebastian Vettel, Barrichello, Heikki Kovalainen and Mark Webber were involved in serious collisions with each other, while the likes of Kazuki Nakajima and Kimi Raikkonen spun into the wall.
Adding further intrigue, incidentally, BMW Sauber driver Robert Kubica revealed in Monza that Ferrari had also held talks with him about filling in for Massa but that discussions had gone no further.
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