The 37 year-old forward got on the end of Adam Le Fondre's hooked cross to head home the only goal just before the break.
With Tom Elliott absent through injury, Warne was drafted into the starting line up and repaid Ronnie Moore with a workmanlike performance, along with the rest of his team mates.
It could have been a different story for the Bulls, who were wasteful infront of goal particularly in the second period and came up against an in-form Andy Warrington.
Janos Kovacs and James McQuicken both had chances in the opening half hour that flashed past Warrington's upright, and the Millers stopper was also equal to Shaun Canham's header.
Kevin Ellison had Rotherham's best effort on 32 minutes, his cross shot just clipping Kovacs' head and flying wide of the far post before Warne netted going into half time.
Warrington was called upon after the break and produced several fine stops, including a point blank save from O'Neill Thompson.
Thompson also managed to fire wide with a glaring miss on 76 minutes from just eight yards with the goal gaping, and Stuart Fleetwood shot wide of the post as the home side piled on the pressure.
However Rotherham survived an aerial bombardment and five minutes of stoppage time to move into joint second place in League Two.