The Millers went into the game already guaranteed a playoff place, and gave leading scorer Adam Le Fondre a day off replacing him with Drewe Broughton.
There was also a start for Danny Harrison in midfield after his suspension, replacing the injured Josh Walker.
A good following from Rotherham had their party mood spoiled when Hereford went in front after just four minutes, Frenchman Manset scoring past Warrington at his near post after Pugh had beaten Sharps.
It was looking as though the Millers had both eyes on next weeks game in the playoffs rather than this one, when in the twenty first minute Lunt crossed for Jones to put the Bulls two goals up.
The first half came to a disappointing end with the Bartlett in the Hereford goal being a virtual spectator.
Hereford came out of the blocks in the second half much the same as the first with Constantine hitting the post after a couple of minutes.
Drewe Broughton went close as the Millers finally started to come into the game, with Kevin Ellison also having a chance when getting into a good position only to miss the target with his header.
There was a double substitution for the Millers after seventy minutes with Paul Warne and Mickey Cummins being introduced and Drewe Broughtton and Pablo Mills going off.
Nick Fenton had one of the few Millers chances with a header from an Ellison corner but sent it wide of the goal.
With ten minutes to go and the game heading towards a defeat for the Millers, Nicky Law left the field to be replaced by Bell Baggie.
A disappointing display for the traveling fans from Rotherham was wrapped up in the last minute of normal time when Marc Pugh cut in from the right and fired his shot passed Warrington..
Despite this defeat the Millers now go into the playoffs with Aldershot Town over two legs standing in the way of a Wembley appearance.
The first leg at Aldershot will be on Saturday 15th May 2010 with a 6.00 PM k.o.
The return leg at Don Valley will be on the folowing Wednesday 19th May, 7.45pm k.o.