Second-half goals from Adam Birchall and Jason Puncheon saw Rotherham suffer a first away defeat of the season.
Barnet were ahead within a minute of the second half as Puncheon hit a post before Neil Bishop set up Birchill to beat Andy Warrington at his near post.
Rotherham's Ian Sharp and Marc Newsham went close with headers but Barnet sealed victory 10 minutes from time.
Sharp fouled Birchill in the area and Puncheon converted the penalty to end Rotherham's proud away record.
Barnet: Harrison, Devera, Yakubu, Burton, Nicolau, Porter (Carew 46), Bishop, Wright, Puncheon, Norville (Hatch 62), Birchall (Thomas 90).
Subs Not Used: Beckwith, O'Cearuill.
Booked: Burton, Yakubu.
Goals: Birchall 52, Puncheon 83 pen.
Rotherham: Warrington, Cresswell, Sharps, Coughlan, Brogan, Todd (King 74), Tonge, Bean, Peter Holmes (Yates 59), O'Grady, Dyer (Newsham 55).
Subs Not Used: Derek Holmes, Annerson.
Booked: Cresswell, King.
Att: 2,008
Ref: Graham Horwood (Bedfordshire).
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