Italian Andrea Dovizioso was third for Ducati, with world champion Marc Marquez finishing only fourth for Honda after starting on pole position but losing out in the battle off the line.
The result left Rossi on 102 points while Lorenzo, who won the previous race in Spain and is the first rider to triumph twice in a row this year, has 87 after five rounds. Dovizioso is on 83 and Marquez 69.
Marquez's team mate and fellow-Spaniard Dani Pedrosa failed to score on his comeback, having missing the last three races due to arm surgery, after crashing on the second lap. He rejoined in last place and finished 16th.
Lorenzo started in third place, following Dovizioso past Marquez before taking the lead on the opening lap, while Rossi had to fight through from seventh.
Marquez momentarily regained the lead but then ran wide almost immediately, dropping down as low as sixth before regaining fourth.
Lorenzo said his aggressive start had been the key to the race but Rossi, who moved into second place with 16 laps to go and smashed the circuit lap record, had pushed him hard later on.
"I saw Valentino in second place, he really was very quick so I had to push even at the maximum...but changing a little bit my riding style I could survive and finish the race with another victory," he told reporters.
"It's very important for the championship so I am very satisfied."
Rossi, who shook hands with his team mate after they got off the bikes, was happy to have kept his overall lead after taking a gamble with the set-up following difficulties in practice and qualifying.
"We suffered a lot during the practice because I wasn't able to ride the bike at the limit," he said. "It also happened in Jerez. But this time we risked more and for the race did something very different," said the 36-year-old.
"I needed two or three laps to understand but after I had the good pace...had a great battle with the two Ducatis. When I arrived behind Jorge, I tried but today he was too fast. But anyway this is a great result for the championship.
"Solid race, solid ride, I enjoyed it, 20 points. Good job."
(Reporting by Alan Baldwin in London, editing by Ed Osmond)
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