Rotherham beat Accrington Stanley 1-0 at the New York Stadium thanks to a fantastic volleyed goal by Dan Barlaser but that and a solid if unspectacular first 84 minutes were lost in the mayhem at the end of the game.
That was bad enough but the Millers are still under investigation after and an object was thrown from the away section at a linesman when Rotherham were at Crewe Alexandra. It followed another incident in January when Rotherham supporters disrespected a minute's silence at Fleetwood Town.
"The talking point - which will be the talking point and possibly not the lads' performance - is the penalty and the fan lad running on the pitch, which I find hugely embarrassing and it's completely unacceptable," said Warne.
"I apologised to all their staff, although it seems quite empty when you've won, but it is abhorrent.
"I apologised to heir captain, he was very emotional.
"It's tainted a good win because three points are three points and I had two centre-halves come off the pitch when we made the subs, Smudge (Michael Smith) had to go at the back and the lads gave everything but I just think the game will be remembered for the wrong reason, not for how hard the lads tried to win a game.
"It's not the players' fault someone came on the pitch and I'm hugely embarrassed by it. I think my moral compass is very good and it just taints a good performance and a good win.
"Everyone's going to be talking about that. Whatever happens on Quest or Sky Sports News, that's going to be the big drama.
"I also feel their pain because if it happened to me or one of my players I would also feel disappointed with it.
"But there were 9,000 Rotherham fans here today and one or two misbehaved at that level. It makes all of our fans look bad and that isn't the case, they're good people who are passionate about their club but a couple of them have just spilled over into unacceptable behaviour and that isn't what we want as a club, it's not who we are."
Rotherham lost Michael Ihiekwe through injury before RIchard Wood was sent off for handball in the incident which brought about the penalty. Warne was in the toilet when it happened, but from what he had heard about it, had no complaints with the decision.
With eight minutes added to the game, it was frantic from the moment the ball struck Wood's hand, and Warne admitted he was grateful his side did not lose, never mind that they won.
"I think it's the luckiest 10 minutes I've ever spent stood in the dugout.
"We've had really late goals against us in my five years, really unluckiness - I remember Angus (MacDonald's red card) against Norwich, a deflected goal and all that, whereas today I was thinking, 'The net's going to go in a minute,'" said Warne.
"I didn't get myself too stressed because I just kept thinking the goal was going to come.
"At one point I admit I thought I'd take a point we were so under the cosh but for some reason we lived a charmed life.
"It would have been a lot nicer had Wilesey (Ben Wiles) scored on the counter (in the second added minute). Two-nil would have been a lot nicer but it's not my players' fault what's happened, they've given their job lot - two centre-halves down, my centre-forward playing at the back. From the lads' point of view, I don't think we could have done a lot more to try and win it."
Warne's opposite number John Coleman was understandably upset by events, and said he thought the game should have been abandoned.
"I have never seen anything like that in my life," he said. "I was expecting the game to be abandoned.
“It is one of those situations where Pelly is desperate to take it because he has been assaulted as well. Was it the right thing to do? It's easy to be wise after the event. He hasn't meant to miss the penalty.
“I feel physically sick. I am beat and I have nothing more to offer. I can't fight back. I can't criticise. I am proud of how the players played today.
“It was a classic away performance. In the second half we gave everything we've got. We tested their keeper and hit the post late on. We didn't deserve to lose the game, but we have.
“I am sure the authorities will do what they have to do.”
Ihiekwe's injury came from a clash of knee and he must now be a doubt for Tuesday's trip to Wimbledon, which Rarmani Edmonds-Green is injured for. Wood will be suspended, although he will be back for the weekend derby at Sheffield Wednesday.
With Wigan Athletic playing in the FA Cup and Sunderland surprisingly beaten at home to Doncaster Rovers, Rotherham's position in the league table is at least stronger - so long as they do not suffer a points deduction for a third incident of crowd misbehaviour in a month.