O'Neill, whose side lost 3-0, thought the defender should have been sent off for the second-half tackle on his England team-mate and launched an emotional attack on the quality of refereeing in the game.
Referee Howard Webb also denied the Birmingham side a penalty 16 minutes into the first half when Chelsea midfielder Jon Obi Mikel manhandled Gabriel Agbonlahor to the ground inside the area.
But the usually even-handed Irishman's strongest words were reserved for Terry's challenge on Villa midfielder Milner.
"James is very sore and he's very lucky," O'Neill said. "He's exceptionally lucky to have his career intact."
"His leg was in the air at the time which helps. It was desperately poor, a desperately poor challenge, and it should have resulted in a red card with 15 minutes to go and at 1-0."
O'Neill's anger at unfair refereeing followed February's League Cup final which they lost to Manchester United also at Wembley. On that occasion the referee failed to send off defender Nemanja Vidic who gave away an early penalty.
"I know there are decisions in games and in matches we can all contest," said O'Neill. "It happens in a match and I accept these are incontestable decisions.
"Today we don't get a penalty because the consequences are in referees' minds," he added. "Just apply the law that's what I'm looking for - a bit of fair play."
O'Neill said he had the "utmost respect" for Webb before attacking his decision-making once again, saying: "It was a clear sending off and that's a major decision."
DESPERATELY UNLUCKY
Chelsea scored through Didier Drogba in the 67th minute after a turgid first half marred by the penalty claim but light on entertainment or other real scoring chances.
Florent Malouda and Frank Lampard added goals in the dying minutes to add insult to O'Neill's perceived injury.
"Five weeks ago a referee bottled it against Manchester United," O'Neill said. "Maybe we've been desperately unlucky. Twice we come here and we've had major decisions go against us. The point is they're game-changing and it was straightforward."
He added his side came to Wembley with real hopes of winning despite a 7-1 Premier League defeat by Chelsea two weeks ago.
"At half time, I thought there was nothing in it - I thought we could win," he said. "It was an injustice today and I thought it was an injustice five weeks ago.
Chelsea manager Carlo Ancelotti admitted he was relieved his side had won after a poor first half showing. He also did not deny Villa might have had a spot kick in the first half.
"It could be a penalty, it might not be, it was a strong tackle in the penalty box."
He also declined to speculate on Chelsea's chances of winning the FA Cup and League double.
"I don't want to speak about 'if' I am very focused on the next game, we are very close to winning but we have not won anything yet. We have to work hard for one mo
