But Harte has revealed that the Tyrone skipper is "back in training for about eight or 10 days", and is ready to play a full role in Saturday night's clash.
O'Neill has endured a luckless season with injury after missing out on the Allianz League Division 1 final clash with Dublin after incurring a freak ankle injury having inadvertently stepped on a football during Tyrone's warm-up.
And he could be joined in their starting XV by defender Dermot Carlin, who suffered the misfortune of breaking his nose twice in a week almost six weeks back. Saturday night's live televised game will be the only one of the third round to involve any team from Division 1 of the league. During their top-flight campaign, Tyrone beat Kildare in Newbridge and also in Croke Park in the semi-finals of the competition.
However, Harte insisted that, "Kildare's record in the qualifiers under Kieran McGeeney is quite awesome", adding that he had total respect for his opposite number.
"I think he was a great player. I had total respect for him as a player and as a manager. He's one of those people with whom what you see is what you get and it is very hard to beat that."
The winners on Saturday night will face beaten Leinster finalists Meath in the fourth round of the qualifiers for a spot on the August Bank Holiday weekend – a position Harte insisted he believed his team would end up in immediately after being beaten by Donegal in the Ulster first round.
"If I'm not confident that we can do that, then how are the players going to be confident that they can do that?" he reasoned.