It meant the Millers emerged from their “week of death” with one win and back-to-back defeats, and leaves them four points from safety with two games in hand on Derby County.
Whilst Birmingham manager Lee Bowyer was refusing to take safety for granted, it nudged the Blues closer to being out of the equation.
It was a huge blow but not, Rotherham's manager was keen to stress to them, a fatal one.
The Millers had much the better of a low-quality game, but were unable to put any of their 17 chances away. Harlee Dean's 89th-minute header ensured they did not even have a point to show for their efforts.
“If this game had been in October and we lost 1-0 I wouldn't have been as sick but I appreciate every single point we fight for now has an increased intensity,” acknowledged Warne.
“But I can take positives. After Thursday night I asked the lads too play it like it was the last game of their careers and I just thought they did themselves much more credit today.
“I was disappointed on Thursday night, our performance wasn't acceptable, really. I appreciate why.
“Our performance today was good, fundamentally we just didn't take our chances. We had enough attempts on goal and enough half-chances to at least get something but if you don't score at this level there's always the opportunity you're going to get done.
“We'd limited Birmingham to very few chances. We knew their threats on long throws and diags and I thought the lads defended well.
“We didn't deserve to be on the losing side of that.”
With another home game – their fourth in a row – against a Middlesbrough side led by Warne's old Rotherham manager Neil Warnock on Wednesday, the Millers cannot afford to dwell on their misfortune.
“I have to go in (to the dressing room) after trying to pick myself and my staff up to say to the lads you're still in it,” he said. “As soon as you lose your belief, you might as well not turn up.
“I'm not saying it doesn't make it harder. Three points or even a point would have been great.
“We go to Middlesbrough and if we manage to get a win there it looks great. I feel for them because there's nothing I can say to them to make them feel better. All the lads are hurting, me included.”
The game was Rotherham's fourth in eight days, a schedule Birmingham manager Lee Bowyer called “crazy”.
“I feel for them,” said the former Leeds United midfielder. “To play Sunday, Tuesday, Thursday is crazy but we have to finish when we do and there's no other space.
“They looked a bit tired at the end, which is understandable.
“We knew it was going to be a tight game, two teams pushing each other wanting the three points, the same formations cancelling each other's out a bit.”
Warne, though, was delighted with the effort his side showed.
“I've got nothing but respect for the lads, you could see they were jaded nearer the end,” he said. “They gave everything we possibly could.
“We were forced into a change with Robbo (Clark Robertson) because he was fatigued, I thought Shauny Mac (Shaun MacDonald) was fatigued a little bit and I thought Hirsty (George Hirst) might give us something else up top but apart from that the lads had to stay out there and fight. There's no complaints from me in that respect.”
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