The Spaniard's best lap of 1m35.391s was still slower than the benchmark set by Massa in second practice on Friday. The Brazilian was second quickest on Saturday morning, over six tenths behind his team-mate.
Lewis Hamilton finished third for Mercedes as team-mate Nico Rosberg had to settle for 14th position after being unable to set a time with the soft Pirelli tyres.
World champion Sebastian Vettel outpaced Red Bull team-mate Mark Webber for the first time this weekend to finish in fourth position, right ahead of the Australian, who completed the top five.
Force India's Adrian Sutil was sixth ahead of the first Lotus of Kimi Raikkonen, McLaren's Jenson Button and Sergio Perez and the Sauber of Nico Hulkenberg, who rounded up the top 10.
Caterham's Charles Pic and Giedo van der Garde were the first men to appear in the timesheets, the duo the only men to post a timed lap in the first 10 minutes of the session.
Perez jumped to the top of the times nearly 20 minutes in, becoming the first driver from a top team to set a time. He was promptly outpaced by Romain Grosjean in the Lotus, the Frenchman relegated by team-mate Raikkonen just moments later.
With a quarter of final practice gone, it was FP1 pacesetter Rosberg who moved to the top with the first 1m37s lap of the hour-long session. Team-mate Hamilton bettered his time three minutes later as Vettel went second quickest behind the Briton, both men still far from the leading times from Friday.
Hamilton was first to move into the 1m36s at the half-hour mark, while Rosberg put the other Mercedes in second position ahead of Vettel.
Ferrari drivers Alonso and Massa waited until the second half of the session to complete their first timed laps, the Spaniard moving to fifth spot 28 minutes in with used medium tyres. Friday pacesetter Massa went sixth quickest with his first attempt seconds later.
The soft tyres made their appearance with less than 20 minutes left, with Rosberg and Raikkonen the first of the frontrunners to try the yellow-marked rubber.
The German, however, aborted his first attempt and complained about excessive bottoming, returning to the pits without setting a time. His mechanics started working on the car immediately and he would not return to the track.
Team-mate Hamilton also slowed down right after posting the quickest time in the first sector, also using soft tyres, but the Briton continued for another run.
Although his first sector was not as strong as before, Hamilton posted the best time of the session with a lap of 1m36.065s which put him over a second clear of the rest of the field at the time.
With most teams eager to save their soft tyres, the action was sparse as the session reached the final 10 minutes. Raikkonen jumped to second with eight minutes to go, but the Finn was still over half a second off Hamilton's pace. He was soon outpaced by Sutil, but the Mercedes driver's time was still out of reach.
Most drivers finally jumped onto the circuit with five minutes left, Alonso setting the fastest time of the day with a 1m35.391s, still slower than Massa's best from Friday. The Brazilian moved to second ahead of Hamilton.