Alonso's world title hopes are resting on a knife-edge going into the season-ending Brazilian Grand Prix on Sunday, with the Spaniard 13 points adrift of Sebastian Vettel.
The 31-year-old needs to qualify high on the grid in his Ferrari to give himself a fighting chance of overhauling Vettel, both on track at Interlagos and in the championship standings.
But Alonso found himself half a second adrift of pacesetter Jenson Button in his McLaren, the Briton setting a blistering lap of one minute 13.188secs to edge out Vettel and keep his team on top.
The 25-year-old German was just 0.057secs adrift of Button and 0.140secs ahead of Red Bull team-mate Mark Webber, with Lewis Hamilton in close attendance to the Australian in his McLaren.
Hamilton, in his final race for the Woking-based marque before he moves to Mercedes on a three-year deal from next season, had been quickest in both of Friday's sessions.
But in the closing hour-long run ahead of qualifying the 27-year-old had to play second fiddle to Button as he was two tenths of a second off the pace.
Crucially for Alonso, Lotus and Force India appear to have found some speed as Romain Grosjean, Paul di Resta and Nico Hulkenberg relegated the double world champion into that eighth place.
Williams' Pastor Maldonado and Ferrari team-mate Felipe Massa were also hot on Alonso's heels, which could make for a nervy qualifying session for the 31-year-old.
In the second Lotus, Kimi Raikkonen endured further trouble after encountering niggly issues on Friday, the Finn finishing bottom of the standings and failing to set a time after he coasted to a halt with engine trouble.
Mercedes, meanwhile, slipped to 12th and 15th via Nico Rosberg and Michael Schumacher, the latter inconspicuous in his last practice outing before retiring for a second time, finishing 1.1secs down.