Terry Butcher secured his first win as Brentford boss in a fiery derby match.
Brentford debutant Lee Thorpe was shown a red card for a first-half lunge and Barnet's Stevland Angus went in the second half for fouling Ryan Peters.
Kevin O'Connor put Brentford ahead with a penalty following a disputed decision when Charlie Ide's run was ended.
Jason Puncheon equalised, but the hosts sealed victory when Angus fouled Peters and John Mousinho followed up after O'Connor's spot-kick was saved.
Brentford: Hamer, Starosta, Mackie, Osborne, Basey, Pettigrew, Ide (Peters 58), O'Connor (Poole 85), Moore, Mousinho, Thorpe.
Subs Not Used: Simon Brown, Smith, Pead.
Sent Off: Thorpe (45).
Goals: O'Connor 50 pen, Mousinho 71. Barnet: Harrison, Hendon, Burton (O'Cearuill 48), Angus, Nicolau, Porter, Seanla, Leary (Hart 20), Puncheon, Thomas, Birchall, Hart (Hatch 72).
Subs Not Used: Beckwith, Grazioli.
Sent Off: Angus (70).
Goals: Puncheon 61.
Ref: Paul Melin (Surrey).