Mercedes had a disappointing day after Nico Rosberg and Lewis Hamilton started on the front grid.
Rosberg squeezed into the final qualifying session in 10th but could barely improve with ninth place.
Schumacher cannot be world champion again if Rosberg is in front of him all the time.
Schumacher's 1:12.947 put him well ahead of Rosberg, who was fourth best on 1:13.543.
The same penalty befell Nico Rosberg after he made an illegal manoeuvre exiting the pit lane.
Barrichello finished sixth behind Williams's Nico Rosberg and Jenson Button while Lewis Hamilton was last.
"It's one clear option less, that's pretty obvious, but I am still very pleased with my situation, " said Rosberg.
Heidfeld and Rosberg both drove unobtrusively excellent races to take the final two podium positions.
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Rosberg's third place was the best result of his career in his third full season.
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Rosberg said Williams were keen to keep him but hinted he would leave.
Rosberg has also been impressed by the hunger for success at Mercedes after a lackluster 2012 season.
Schumacher's Mercedes team-mate Nico Rosberg is destroying him in both qualifying and the races, by and large.
Toro Rosso's Sebastien Buemi claimed sixth ahead of Williams' Nico Rosberg, with BMW Sauber's Robert Kubica eighth.
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Schumacher's team-mate Nico Rosberg ended up in sixth place in an incident-packed race after qualifying in 10th.
The car was uncompetitive and Schumacher was out-paced for much of the year by team-mate Nico Rosberg.
The German's team-mate Nico Rosberg finished fifth to cap off a good weekend for Ross Brawn's team.
Rosberg, meanwhile, is fifth on 67 points and clinched the first race win of his career in China.
Renault's Robert Kubica and Mercedes' Nico Rosberg were next, ahead of Webber, Force India's Vitantonio Liuzzi and Alonso.
Rosberg has been linked with a move to F1 with Williams where his father won the world title.
Rosberg was the first driver to get behind the wheel of the F1 W03 at Silverstone last week.
Rosberg, son of 1982 Formula One world champion Keke, is out of contract with Williams at the end of the season.
Defending world champion, Sebastian Vettel finished fifth in qualifying while his compatriot, Mercedes driver Nico Rosberg is sixth.
Mercedes driver Nico Rosberg, son of Finland's 1982 world champion Keke Rosberg, can boast that he grew up there.
In the afternoon, Williams's Rubens Barrichello was seventh ahead of Kubica, the second Williams of Nico Hulkenberg and Rosberg.
"Sixth place was probably the best result that we could have achieved today, so I'm pretty happy, " said Rosberg.
"For me, to have him here is a great thing, fantastic, " Rosberg told reporters about his alliance with Schumacher.
Nico Rosberg of Mercedes finished seventh with rookie Paul Di Resta in eighth in the second Force India car.
Nakajima's team-mate Nico Rosberg was ahead of the Japanese when he retired with an engine failure on lap 42.
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Nico Rosberg, who was fastest in final practice, claimed fifth spot ahead of Ferrari's Felipe Massa and McLaren's Heikki Kovalainen.
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