Reserve Brigadier General Yiftah Spector was sacked from his post at the air force training academy by air force commander General Dan Halutz after refusing to retract his views, Israeli media reported on Wednesday.
Spector was the most senior of the 27 pilots who signed the petition last month, in which they said they no longer wanted "to obey illegal and immoral orders". They said they refused "to take part in aerial raids against populated civilian centres" in the West Bank and Gaza Strip.
"The continuation of the occupation endangers the security of the state of Israel, as well as its moral fibre," the pilots added in their letter.
The petition has attracted the support of Israeli peace activists and a group of academics but infuriated top brass.
Halutz replied to the pilots in a harsh letter in which he accused them of having "shoved a knife in the back of combatants and of Israeli democracy".