The 10-man Millers, who had Angus MacDonald sent off in the first half, slipped to their heaviest defeat of the season and suddenly their place in the top two is under threat.
Warne’s side are now just four points above third-placed MK Dons with eight games to play. It is still a good cushion to have but the gap was 10 points just a few weeks ago.
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Wigan are also now big favourites to win the title after they won again and they look set to displace the Millers at the summit by the time they play again on March 9.
Warne’s side were already trailing to Daniel Udoh’s opener when MacDonald was controversially sent off for an elbow on Luke Leahy before half-time and things got worse after the break as Elliott Bennett and Ryan Bowman made it a comfortable afternoon for the hosts.
Rotherham’s three-week break from League One action has come at a good time, allowing them to recharge their batteries and reset after a difficult period.
The Millers boss hopes that his side can recover from the loss and use it to get over the line.
“I think the players are ready for a break,” he said.
“I appreciate that our job is to entertain the fans, they come in and want to win, as do we, we do everything we possibly can to win the game.
“Today we just weren't good enough and I didn’t rant and rave and throw bottles.
“I just told them to have a couple of days away, enjoy themselves, don't think about football and then we will just come in and refresh.
“The lads have been excellent, in fact we have been spoiled today at how good we have been. We have lost today, the two teams below us have won.
“Is this a massive turning point? Maybe. Maybe at the end of the season we will look back at this result and say it kicked the lads on.
“Or maybe it goes the other way, who knows. All we can do is be really positive around the group, be really proud of how well they have played and how well they have fought throughout the season.
“We are still in a really good position, not as good as it could have been, obviously.”