The incident cost Hamilton the championship lead, which has now been assumed by Kubica.
Hamilton's exit threw the race wide open, but Kubica always had the upper hand.
Kubica's team-mate Nick Heidfeld and the second Toyota of Jarno Trulli completed the top 10.
BBC: Hamilton edged out Ferrari's Kimi Raikkonen by 0.102secs
The Englishman never looked back as he finished some 12 seconds ahead of Kubica.
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
The impact saw the guard rail break the drivers' side door and cause the injuries to Kubica.
Sebastian Vettel's Red Bull and Robert Kubica's BMW Sauber suffered engine problems on day one in Monte Carlo.
Kubica survived an intervention by the safety car and a crumbling track that provoked errors from several drivers.
Renault's Robert Kubica and Mercedes' Nico Rosberg were next, ahead of Webber, Force India's Vitantonio Liuzzi and Alonso.
Domenicali described Kubica as a great driver, but stopped short of confirming or denying Ferrari's interest in him.
Citroen team principal Yves Matton said Kubica deserved to succeed in his comeback because of his fighting spirit.
Removal of the two driver aids was weighing on a number of minds, including Heidfeld's team-mate Robert Kubica.
"It was a shame because he got out in front of Kubica, and was looking OK, " added Brawn.
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.
In the afternoon, Williams's Rubens Barrichello was seventh ahead of Kubica, the second Williams of Nico Hulkenberg and Rosberg.
Kubica spent nearly three months at the Santa Corona hospital in the town of Pietra Ligure following the crash.
Glock had been tipped as a potential team-mate for Robert Kubica at Renault.
Kubica was ruled out of the entire 2011 campaign after sustaining serious injuries following a preseason rally crash in Italy.
Do I think Schumacher can take on Vettel, Alonso, Hamilton, Button and Kubica over a long season and be champion?
Heidfeld, a veteran of 172 grands prix and a former team-mate of Kubica, wasted no time in proving his credentials.
BBC: Nick Heidfeld heads Fernando Alonso at his Renault test
The yellow safety flags came out after a collision between Red Bull's Sebastian Vettel and Robert Kubica in his BMW Sauber.
Kubica's co-driver, Jakub Gerber, was unhurt in the incident, which occurred as he lost control of his car on a bend.
The McLaren driver clocked one minute 17.886 seconds to better Robert Kubica's mark for BMW Sauber by more than half a second.
Felipe was battling with (Robert) Kubica and I was with (Vitaly) Petrov.
Kubica, who has two second-place finishes this season, also played down his chances of capitalising on his front row position on the grid.
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