Ferrari's Brazilian Felipe Massa was third fastest ahead of Italian Giancarlo Fisichella who qualified fourth in a Renault, while German born Nico Rosberg was fifth for Williams and will share the third row with Australian Mark Webber in his Red Bull.
German Nick Heidfeld was seventh ahead of his BMW Sauber team-mate Pole Robert Kubica with the Honda pair Brazilian Rubens Barrichello and Briton Jenson Button ninth and 10th.
After several days of fine, warm weather, Saturday was cold, wet and windy, with morning practice run in rain-hit conditions and the afternoon qualifying beginning in similar unpredictable conditions.
Hamilton was fastest after the opening mini-session ahead of Alonso, with Finn Kimi Raikkonen third for Ferrari, however at the other end of the time-sheets, the bottom six were eliminated from qualifying, meaning Dutchman Christijan Albers in a Spyker, and Japan's Takuma Sato, in a Super Aguri, would start from the back row of the grid.
Ahead of them will be Adrian Sutil, who was unable to repeat his feat of being fastest in the morning session, and German Ralf Schumacher in a Toyota, with Briton Anthony Davidson in the second Aguri car, and American Scott Speed in a Torro Rosso.
Raikkonen car trouble
The second mini-session saw Hamilton continue to set fast lap times, but an incident in the early stages appeared to upset Ferrari plans to mount a fight-back, as Raikkonen damaged the steering on his car and the front right wheel looked to be knocked askew in his first run.
This resulted in the Finn coming to a halt at a bad angle across the circuit at the Rascasse hairpin and partly-blocking the circuit ahead of his team-mate Massa, who was forced to take avoiding action to pass him.
Raikkonen's car was transported back to the pits for repairs, but after the problems the Ferrari driver could only manage to finish down in 16th place and out of the running.
This meant that the Finn was destined to start from the eighth row of the grid alongside compatriot Heikki Kovalainen with another former Monaco winner Jarno Trulli of Italy ahead of them for Toyota alongside Liuzzi.
Coulthard punished
The other two men ousted were Briton Jenson Button in his Honda and Austrian Alex Wurz in his Williams. They qualified on the sixth row, but like the others eliminated in the second session were to find their fortunes altered.
An announcement by the stewards at the end of the second mini-session made clear that David Coulthard was punished for a qualifying misdemeanor and was not permitted to take part in the third mini-session.
He was left in 10th place, soon after amended to 16th a decision that meant everyone else was shuffled up a place and that Button was back in the action in the final session.