The 27 year old lapped the Valencia street circuit with a best time of one minute 40.890 seconds on a gusty and overcast morning with temperatures cooler than they had been the previous day.
Sebastian Vettel, Red Bull's double Formula One world champion who is chasing a hat-trick of Valencia victories this weekend that would also end a run of seven different winners in seven races, was second fastest and 0.083 slower.
Mark Webber, Vettel's Australian teammate who spent part of the session watching his mechanics fix an hydraulic problem with the car's rear wing DRS system, was third quickest.
McLaren's Jenson Button, whose form has plunged since he won the season-opener in Australia, was fourth on the list in a sign that he may have found a solution to at least some of the setup problems.
Ferrari's Fernando Alonso, competing in front of his home Spanish crowd for the second and last time this season, was fifth on a trouble-free morning.
Michael Schumacher, Mercedes's seven-time champion, lapped seventh fastest while championship leader and Canadian GP winner Lewis Hamilton was eighth for McLaren.
There was little track action for the first half hour on a dirty track, with drivers doing installation laps only and ducking back into the pits without roaring down the main straight.
Maldonado, whose recent results have suffered after he was hit with three grid penalties in two races, posted his best just over half way through the 90 minute session and it stood the test of time.
In an indication of how close Sunday's race could be, with overtaking always difficult and pole a huge advantage, the top nine drivers were separated by less than three tenths of a second.
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