The Brazilian lapped the Circuit de Catalunya with a best time of one minute 21.901 seconds, just 0.006 quicker than Lotus's Kimi Raikkonen.
Red Bull's Australian Mark Webber, who has been on pole twice in the last three years in Spain, was third fastest on a generally bright morning with a lap 0.143 off the pace.
McLaren, who triggered headlines suggesting they were relying on "a wing and a prayer" after rushing two new front wings to the circuit overnight after a major aerodynamic update proved disappointing on Friday, appeared no closer to the Formula One front-runners.
Britain's Jenson Button finished 12th and Mexican Sergio Perez 14th. Button was 1.250 slower than Massa.
A team spokesman said the new wings were not used in practice and were unlikely to be on the car in qualifying either.
Sebastien Vettel, Red Bull's triple world champion and overall series leader, was fifth fastest, behind Lotus's Frenchman Romain Grosjean after setting the best time on Friday.
Massa's team mate and local favourite Fernando Alonso was sixth.
Vettel leads Raikkonen, who can become the first driver to win three times in Barcelona with three different teams, by 10 points after four races.
Qualifying is crucial in Barcelona, with 18 of the past 22 races at the circuit won from pole and only one driver winning without starting on the front row.
Venezuelan Pastor Maldonado, who won from pole last year for Williams, was 15th on the timesheets as the former champions struggled with a car that has yet to score a point this year.