The Fiat Yamaha rider, who boasts an outstanding record of two pole positions and two podiums from his two
MotoGP starts, worked on set-up and tyre testing for Michelin during his 94 laps.
And the 20-year-old not only topped the time sheets on a qualifying tyre, by 0.438secs over Bridgestone-shod team-mate Rossi, but also lapped consistently fast on race tyres.
Lorenzo's best time on a race tyre was 1min 39.59secs, over half a second under Pedrosa's lap record set in Sunday's race.
"It was another really good day today; Jorge's progress is almost unbelievable for us to watch and every day is enjoyable," declared team manager Daniele Romagnoli. "The most impressive thing today is that we were able to improve on Jorge's race pace from Saturday, which was the best pace of the whole weekend.
"We continued to work on set-up and improved the front feeling with the help of a new fork setting, and with race tyres today he was very consistent and very fast. We also refined some engine mapping and through this it seems that we've been able to obtain improvement with tyre wear.
"Michelin had planned a very interesting tyre test for us today with Estoril in mind and we found some good things, especially concerning the rear tyre. Jorge has done a great job at just his second race and today's test gave us a chance to check out some important things that will help us at the next race in Estoril.
"We're already looking forward to the next challenge but for now I want to thank all the team and Yamaha for their hard work; they deserve a good rest before Portugal," he concluded.
The top seven riders all set their best lap times with qualifying tyres, with world champion
Casey Stoner putting a difficult race day behind him by being best of the rest behind the factory M1 pilots.
Randy de Puniet, who crashed out of the grand prix, was fourth fastest ahead of the lead Kawasaki of
John Hopkins and top Suzuki of
Loris Capirossi.
Shinya Nakano was seventh.
Pedrosa and Repsol Honda team-mate
Nicky Hayden only used race tyres, and were separated by 0.273secs in eighth and ninth.
Stoner's Ducati Marlboro team-mate
Marco Melandri had been hoping to find answers for his early season troubles, but was forced to finish testing early after a minor hand injury.