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The 31-year-old Italian, who has missed four races since the injury last month, lapped the twisty Sachsenring circuit only a fraction of a second slower than Yamaha team mate and championship leader Jorge Lorenzo.
Spain's Dani Pedrosa, who has always been quick at the eastern German circuit, was fastest for Honda in one minute 22.521 seconds, ahead of Casey Stoner on a Ducati and the Australian's American team mate Nicky Hayden.
Lorenzo was sixth fastest with a best time of 1:23.224 compared to Rossi's 1:23.244, with the returning Italian among the top four fastest for most of the session run in temperatures of 36 degrees Celsius.
"Once again Valentino has surprised everyone," said team boss Davide Brivio. "From a team point of view it was like he had never been away, working on the suspension and searching for the best set up.
"His physical condition isn't too bad, a bit more difficult in the right-hand corners and okay on the left, but overall it is a lot better than we expected."
Rossi, who was told by specialists in June that he could expect to be out for four to five months after fracturing his right shin and fibula, was delighted with his astonishing return to two wheels.
"I am a lot more agile on the bike than I was in the tests," he said, applying ice to his injured leg after the session.
"I feel good and this track is helping me because a lot of it turns to the left," added the Italian, whose injury at his home grand prix at Mugello ended a record run of 230 successive starts.
"I am feeling quite confident on the bike and also my shoulder is good and not giving me problems. Now I have some pain in the leg and ankle but it's not too bad.
"We will have to wait until tomorrow morning to see how the leg is and whether it has swelled overnight or developed any problems," said the nine-times world champion, who has slipped to seventh place in the standings.
