Earlier in the session Alonso had spun wildly out of Turn 2 while on a hard tyre run. He stopped just short of the gravel trap and was able to continue.
Sebastian Vettel looked best-placed to depose Alonso at the end, as everyone else fell shot on their medium runs.
The world champion's Red Bull had been on top for most of the session, and waited until the final seconds before heading out on medium Pirellis.
Vettel came across traffic halfway round his lap, prompting an angry gesture at Charles Pic. But even before he encountered the Caterham, Vettel's sector times were already shy of Alonso's.
Running very wide over the rough Turn 12 kerbs then stymied Vettel's next lap and he failed to improve on the 1m33.348s he had set on mediums, 0.101 seconds off Alonso's pace.
Mark Webber completed the top three in the second Red Bull.
Lotus duo Kimi Raikkonen and early pacesetter Romain Grosjean were fourth and sixth, sandwiching Lewis Hamilton.
The Mercedes had a dramatic end to its session when Hamilton suffered an apparent left rear tyre failure on his slowing-down lap. The car sustained suspension damage in the incident, but Hamilton was able to nurse it back to the pits.
Mercedes is now having to carry out a left-rear corner change before qualifying. It is unsure what caused the initial tyre problem.
Force India stayed with the frontrunners as Adrian Sutil and Paul di Resta took seventh and eighth, followed by Nico Rosberg's Mercedes and Nico Hulkenberg's Sauber.
Felipe Massa, fastest on Friday morning, was only 11th for Ferrari, ahead of the McLarens.
At the back, Marussia's Max Chilton had to sit out the latter part of the morning due to a KERS problem.