The Spanish Yamaha rider, who is second in this year's standings behind compatriot Dani Pedrosa of Honda after seven of 18 races, was running quickest in the afternoon session but lost control at turn 10 and landed heavily on his left shoulder.
"The Mallorcan was taken to the Clinica Mobile, where examinations indicated that the eight screws in his shoulder were in tact but that the titanium plate itself had been bent by the impact," organisers said on the MotoGP website.
The 26-year-old had the screws and plate inserted two weeks ago after sustaining a broken collarbone in practice for the Assen Grand Prix and despite the injury flew back to Netherlands after surgery in Barcelona and finished fifth.
After the setback in Germany, he now faces a race to be fit in time for the US Grand Prix at Laguna Seca next weekend.
"I have decided to go home and recover after today's crash at Sachsenring," Lorenzo said on the Yamaha Factory Racing website.
"I prefer to focus on surgery to fix the plate that was unfortunately bent during the crash. I will try to recover and be back as soon as possible."