The German, running on medium compound tyre in his Mercedes-powered VJM09, was 0.728s clear of Renault's Kevin Magnussen, whose best time came on soft rubber.
Magnussen, making his first appearance behind the wheel for Renault, completed 63 laps in the morning session.
Mercedes' Nico Rosberg (1:26.084) was third quickest as he added a further 74 laps to the 172 he managed on Tuesday.
The German will hand his Silver Arrow over to team mate Lewis Hamilton this afternoon after Mercedes altered their run plans because of the "unprecedented mileage levels" completed in the two days thus far. "We want to keep our boys in top shape for Melbourne!" the team added on Twitter.
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Sainz had caused the first of two red flag stoppages when he stopped his car on the exit of the pit lane with a loose rear wheel.
The other red flag was caused by rookie Rio Haryanto, whose 2016 debut was interrupted when he beached his Manor into the gravel at Turn 5. The Indonesian pilot had clocked 25 laps before that.
Having topped the timesheets on the opening two days of testing with Sebastian Vettel, Ferrari had a difficult morning, with Kimi Raikkonen consigned to the garage for several hours.