The double world champion lapped the Mediterranean port's street circuit with a quickest time of one minute 39.404 seconds, despite an earlier collision with BMW-Sauber's Nick Heidfeld.
Brawn GP's Formula One championship leader Jenson Button was second fastest, 0.774 slower than the Spaniard, with Brazilian team-mate Rubens Barrichello third. Barrichello had set the pace in the morning with a time of 1:42.460.
Alonso had been in danger of missing Sunday's race after his Renault team were handed a one-race ban in Hungary last month but the team had that overturned at an appeal hearing in Paris last Monday.
Ferrari stand-in Luca Badoer completed 62 laps, more than a race distance, in the two sessions. The 38-year-old Italian, preparing for his first start in a decade, was more than a second slower than everyone else in the opening session.
(Published 21 August 2009, 17:51 IST)