Robbie Muirhead struck twice as MK Dons boosted their survival hopes and dented the Millers’ promotion bid with their first league win of 2018.
Semi Ajayi fired the Millers, who kicked off sitting in fourth place, into a ninth-minute lead from Caolan Lavery’s ball, but midfielder Muirhead levelled 10 minutes before the break.
There was better to come for the hosts six minutes later when Peter Pawlett put them ahead from close range, and it was he who set up Muirhead to further extend their lead 12 minutes after the restart.
Substitute Jon Taylor gave the visitors hope when he made it 3-2 with 15 minutes remaining, but he could not deny the Dons a first league win in 11 which lifted them to within four points of safety.
“I have no complaints about the result,” said Warne. “We started the game really well and deservedly took the lead. We looked a real threat but for whatever reason, we did not continue to do that and we let them back in and I thought their top-two caused all sorts of problems.
“We had a bad spell in the first half that killed us - 20 minutres of madness cost us basically and I questioned the lads a little bit at half-time and then we had a real go.”
Despite the setback, Warne was pleased with the impact of his second-half substitutes, who gave his side a glimmer of hope of claiming a share of the spoils.
“I was pleased with the way they reacted and the subs went on and made a positive impact,” added Warne.
“It was disappointing when they got the third goal but when we got it back to 3-2, I thought we would get an equaliser. There are some disappointed lads in there but we need to pick them up again for the next game.”
Warne backed his players to return to winning ways soon, starting with Saturday’s trip to Northampton Town.
“It was a disappointing result and we have lost the last two games by one goal, against two teams fighting for their lives,” added Warne. “It’s not a crisis but we need to get back to winning ways very quickly.”