Varun Agarwal, then employed with private carrier Jet Airways, was acquitted because of lack of evidence and the prosecution's failure to prove the case against him, his lawyer said.
"The sessions court has acquitted Agarwal because the prosecution did not bring anything on record to prove the alleged incident," said Agarwal's counsel Laxman Kanal.
The pilot was arrested in May 2010 following a complaint filed by the air hostess, with whom he was in a relationship. He was later granted bail.
According to the victim, Agarwal had promised to marry her but later reneged on the promise. In the complaint, the air hostess accused him of rape and cheating, among other offences.