Centre-back Michael Ihiekwe, Dan Barlaser and Freddie Lapado did the damage as the Millers stretched their unbeaten league run to eight matches.
“It was a pretty damn close faultless display,” praised Warne. “We were not faultless, and there are still things to improve upon, but it was very close.
“We demand a lot out of the group, but they delivered. There were some really good performances out there.”
Captain Ihiekwe pounced for his first goal of the season, heading home in the 27th minute.
And it just got better for the visitors as midfielder Barlaser rifled into the corner through a crowded box for his first goal since December.
It was then left to substitute Lapadop to complete an impressive day at the office with a third goal for the Millers with 18 minutes left, the forward firing home with a sweet strike.
“I’m really pleased,” added the Millers manager. “It was a good away performance against a really good team.
“We had flashes of absolute excellence and that was down to the lads’ dedication. The out of possession stuff was frightening.
“Dan (Barlaser) is a good kid. He is a bit of a quarter-back for us. He enables the other two midfielders to push on. He enables us to switch the play really quick.
“We like to play with width. It was a really good performance from him and he was chaperoned by two energetic performances from Wilsey [Ben Wiles] and Ollie [Rathbone].”
The only frustration for Warne was getting himself booked in the first half for remonstrating with referee Chris Sarginson.
“I got booked in the first half for the first time,” reflected Warne. “I’m disappointed I got booked. “My mum will definitely text me with her disappointed face and I’ll have to build bridges with my family for the rest of the week.”
Milton Keynes Dons: Fisher, O’Hora, Darling, Lewington, Kioso, O’Riley, Kasumu, Jules (Watson 60), Boateng (Parrott 64), Eisa, Twine. Unused substitutes: Martin, Baldwin, McEachran, Ravizzoli, Watters.
Rotherham United: Vickers, Edmonds-Green, Ihiekwe, Harding, Barlaser (Odoffin 82), Ogbene, Rathbone, Wiles, Ferguson (Miller 71), Smith, Grigg (Lapado 64). Unused substitutes: Johansson, Wood, Sadlier, Kayode.
Referee: Chris Sarginson (Stafforshire)