Andy Robinson's late goal wasn't enough for Tranmere as a goal either side of half time from Alex Revell earned Rotherham a 1-2 win at Prenton Park.
There was one change to the team that beat Crewe with James Wallace returning from suspension in place of Jason Koumas.
After a slow start to the game, Rotherham had the ball in the Tranmere net in the 11th minute, but Wes Thomas was ruled offside from Ben Pringle's cross and the game remained goalless.
The Rovers defence had to block a couple of long range shots while Millers keeper Adam Collin had to tip a Jake Cassidy cross away from his cross bar on 13 minutes.
Owain Fon Williams dived to his right to keep out a shot from Thomas on 19 minutes and the keeper punched a swerving 25 yard shot from James Tavernier away from goal eight minutes later.
Claude Davis headed a left wing cross over the bar following a corner in the 36th minute and the visitors' pressure paid off on 39 minutes. Fon Williams palmed a long range effort from Lee Frecklington behind for a corner which he punched clear of the area. However the ball was quickly played to Thomas who raced into the area and squared for Alex Revell to fire in from 12 yards.
It wasn't far off two on 42 minutes. A long throw from Kari Arnason was only cleared as far as Frecklington who side stepped Steve Jennings before curling just over the top left corner from 20 yards.
Rovers had a chance to level on 44 minutes. Cassidy flicked a long ball from Evan Horwood into the path of Ryan Lowe who shot past Collin but his effort lacked power and Tavernier raced back to clear from just in front of goal.
The final chance of the half saw Agard take advantage of a couple of ricochets to run through on goal but he went down under a challenge from Matthew Pennington and the referee rejected appeals for a penalty.
It should have been 0-2 in the first minute of the second half, but after Revell turned Pringle's left wing cross across the six yard box Thomas side footed wide from right in front of goal.
Wallace picked up possession on the halfway line and drove towards the Rotherham defence on 48 minutes but as he reached the Millers area Arnason blocked his path and cleared.
Fon Williams saved from Agard on 55 minutes and Milsom fired wide from the follow up as the visitors continued to dominate.
On 64 minutes they doubled their lead. A long ball forward from Arnason bounced into the path of Thomas and though Fon Williams did well to save his shot, the ball went out of the area to Revell who drilled a shot past three Tranmere players into the roof of the net from 20 yards.
Revell shot past the left hand post from the edge of the area on 70 minutes, while Cole Stockton, on as a substitute in place of Matthew Kennedy fired over from 30 yards nine minutes later.
Substitute Andy Robinson headed Rovers back into the game when he netted from close range after Taylor headed a Koumas corner against the bar.
And there was almost an equaliser when Wallace headed another corner goalwards but Collin pushed the ball away to safety deep in added time.
Tranmere: Fon Williams, Pennington, Taylor, Arthurworrey, Horwood, Kennedy (Stockton 78), Wallace, Jennings (Koumas 73), Kirby (Robinson 59), Cassidy, Lowe. Substitutes: Mooney, Holmes, Goodison, Power.
Rotherham: Collin, Arnason, Davis, Frecklington (Vuckic 88), Revell, Bradley, Pringle, Agard, Thomas (O'Connor 82), Tavernier, Milsom (Smallwood 71). Substitutes: Thompson, Skarz, Turgot, Hitchcock.
Referee: Darren Drysdale