A poor second half performance saw the Millers slip to their first away defeat of the season to leave manager Mark Robins far from happy.
There were three team changes with new signing Ryan Cresswell coming in for his debut while Ian Sharps and Chris O'Grady both returned.
Kicking down the prodigious slope United were the first to make a telling attack with a good ball from O'Grady but Bruce Dyer was just caught offside before O'Grady was stopped in the same way as he tried to get on the end of a Peter Holmes free kick.
A corner and a Steve Brogan free kick brought no reward as the Millers continued to dominate the play and they went close to taking the lead on 21 minutes. A long kick from Andy Warrington found Andy Todd who was fouled just outside the penalty area but Brogan curled his free kick just wide.
Dyer lost possession in a promising situation following a good ball from O'Grady before the home team at last launched an attack in the 28th minute that was stopped by a fine Sharps tackle.
A home free kick was knocked out for a corner that was cleared but back came the Millers again with a long throw from Cresswell that was flicked on by O'Grady. The home defence were struggling to get the ball away but Todd just failed to force the ball home from close range.
Another Cresswell throw saw Sharps flick the ball on and this time Dyer put an effort only just wide.
Just before the interval Barnet had a good chance to snatch the lead when Norville and Nicolau combined well to set up Birchall but Warrington did well to block his close range effort.
The second half opened with Barnet on the attack and after just two minutes they almost took the lead but Puncheon missed a great chance from close range and when the ball was played back in Warrington saved a Carew shot.
Peter Holmes fired a 25 yarder over the bar but the home team's pressure paid off on 52 minutes when Bishop's pass beat the offside trap and Birchall moved inside to score.
A Brogan free kick on 56 minutes was saved and from another Sharps headed wide before a Jamie Yates good cross found Marc Newsham whose header was saved. But back came the home team again with Wright shooting just wide following a cross from the left.
Barnet were doing virtually all the attacking and they forced four corners in quick succession that kept the Rotherham defence at full stretch before a Millers breakaway saw another Brogan free kick headed out for O'Grady to latch on to but his shot from 20 yards was just over the bar.
Any hopes United might have had of snatching a point disappeared on 82 minutes when a high ball into the penalty area saw Liam King commit a foul and Puncheon duly cracked home from the spot to seal the home victory.
A late Rotherham corner brought no reward while the same happened at the other end to crown a very disappointing second half performance by the Millers.
Barnet: Harrison; Devera, Yakubu, Burton, Nicolau; Porter (Carew 46), Wright, Bishop, Puncheon; Norville (Hatch 61), Birchall (Thomas 90). Subs: Beckwith, O'Cearuill.
Rotherham: Warrington: Cresswell, Sharps, Coughlan, Brogan; Todd (King 74), Tonge, Bean, P. Holmes (Yates 59); O'Grady, Dyer (Newsham 56). Subs: Annerson, D. Holmes.
Referee: Graham Horwood (West Yorkshire).
Attendance: 2088 (331 away).
