Jorge Lorenzo, who took his first MotoGP victory at Estoril last year, picked up where he'd left off during Friday practice for the 2009 event.
Dressed in a special silver and white Fiat Punto Evo livery, Lorenzo took over at the top from fellow Spaniard Dani Pedrosa just after the half way mark of the hour - and had extended his advantage to 0.359sec over the Repsol Honda rider by the finish.
Team-mate and title rival Valentino Rossi, who holds a 30 point lead over Lorenzo with four rounds to go, was 0.421sec behind in third, with a returning Casey Stoner fourth for Ducati.
"It's good to be back on the bike after one month but also quite hard! I enjoyed today though and we did a good job and made an encouraging start,” said Lorenzo, a triple 2009 race winner.
“After a bit of work we were able to do a very good time and I am happy to be in front, it's important at this stage of the championship to make a strong start this weekend.
“We have one or two things to improve but we are in good shape. I am happy to see Casey back and also to see that he is already strong.
“Finally I want to mention the special sticker I have on my bike this weekend for Lukas Sembera, a young Czech rider who had a bad accident two weeks ago - I wish him all the best in his recovery."
16-year-old 125GP rider Sembera broke his fourth and fifth vertebrae at the Olympia Supermoto night show. Doctors believe it will be 'very hard' for Sembera to ride again, but it is 'probable' that he'll regain the use of his legs.
“It's impressive how Jorge is already under the circuit record lap and this is great for the first day, especially after such a long break,” said team manager Daniele Romagnoli. “We're quite happy about our performance but now we're looking forward to being able to improve a few small areas even more tomorrow."