Humanitarian groups hailed the decision, saying any conviction would have amounted to criminalizing the internationally-enshrined duty to rescue people from dangerous seas.
In 2004, a ship belonging to the Cap Anamur relief group rescued 37 stranded migrants and then searched for a friendly port for weeks before it was permitted to dock in Sicily.
Former Cap Anamur president Elias Bierdel, ship captain Stefan Schmidt and first officer Vladimir Daschkewitsch were accused of aiding illegal immigration and went on trial in Agrigento, Sicily in 2006.
Defense attorney Vittorio Porzio said the defendants were "more than satisfied" with the verdict absolving them.
The U.N. refugee agency has complained that the trial, as well as recent legislation in Italy criminalizing illegal immigration, has scared fishermen and other boat operators from fulfilling their duties to assist those in need.
Laura Boldrini, a spokeswoman for the U.N. High Commissioner for Refugees in Italy praised the verdict.
"For those who work at sea, it's an encouragement to save human lives, no matter what their judicial status is," she said. "Those who do their duty, and rescue at sea, must not be punished."
Every year, thousands of people, many of them setting out from North Africa, try to reach Italy's coasts undetected. If they don't have proof of a job awaiting them in Italy, they are ordered expelled, although many never leave, authorities say.
Earlier Wednesday, Italy deported 18 Egyptians who came ashore in Sicily a day earlier, the Interior Ministry said.
Italian authorities say smugglers of illegal migrants often take thousands of dollars from their passengers and then either tell the voyagers they are on their own or escape later in motorized dinghies, abandoning the migrants at sea.