The Australian rider's lap of 1 minute, 39.731 seconds was more than one-tenth of a second faster than Yamaha rider Jorge Lorenzo, while his American teammate Nicky Hayden was nearly half a second behind in third.
Valentino Rossi of Yamaha, who won the season-opener at Qatar, was six-tenths back in sixth as the Italian braved back pain sustained in a motorcross accident in early April.
The Spanish GP is the season's second race after the Japanese GP was postponed to Oct. 3 due to air travel chaos caused by the volcanic ash two weeks ago.
Alex Debon of Spain was fastest in the Moto2 category while Derbi rider Pol Espargaro led the 125cc practice.