The home side spurned chance after chance at Windsor Park before David Healy cancelled out Rauf Aliyev's first-half strike in the 96th minute - although a solitary point represents another hammer blow to their already stuttering World Cup qualifying campaign.
"The early goal obviously wasn't in the plan and knocked us a bit," said O'Neill. "But I felt from that moment forward we basically dominated the game, we missed countless chances, but the character the players showed tonight was fantastic and I can't ask any more of them.
"They went right to the death. We saw players playing the last few minutes with knocks and injures. We get the very least we deserved, and we deserved a lot more than that.
"I'm obviously disappointed for the players but I couldn't ask any more of them."
O'Neill was also critical of Azerbaijan's attempts to run the clock down at the end of the match, adding:
"I thought some of the behaviour was not really something you want to see at a football game."
Northern Ireland captain Steven Davis insisted they had been good enough to take all three points.
"We created enough chances to win two or three games but we simply couldn't find the net and when we finally did it was too late.
"I don't think I've played in a Northern Ireland performance where we've created so much, so many clear-cut chances.
"I thought the performance merited the win, but it wasn't to be."