Elias Bierdel, along with captain Stefan Schmidt, and his first officer, Vladimir Dashkevich, were arrested in July 2004 after the vessel Cap Anamur docked in Sicily with the Africans on board.
All three as well as two other defendants were acquitted by a court in Agrigento in Sicily, Bierdel's lawyer, Axel Nagler, told AFP.
"The accused were greatly relieved after this acquittal, especially since the case has taken nearly five years," Nagler said, adding that the court decision clarified that "it was not illegal to rescue people at sea."
The accused had brought the would-be migrants to Sicily after rescuing them at sea between Italy and Malta and then pressuring Italy to admit them. The ship, owned by the organisation Cap Anamur, had first stopped off in Malta, but did not inform the authorities there about the fact that it had the passengers aboard.
Bierdel was criticised at the time for making all the immigrants wear T-shirts with his organisation's logo when they disembarked. He had also been rebuked by the co-founder of Cap Anamur, Rupert Neudeck, who suggested that the rescue operation might have been staged to gain media coverage.
Cap Anamur, headquartered in Cologne, became well-known in the 1980s for rescuing thousands of Vietnamese refugees from boats in the South China Sea.
Italy has become one of the prime arrival points for would-be immigrants fleeing through Africa in search of better lives in Europe. Some 6,760 reached Italy in the first half of this year alone.