Substitute Michael Symes snatched a stoppage-time decider from close-range to earn Shrewsbury only their second victory in 11 matches.
On-loan striker Stuart Nicholson missed a hat-trick of chances and Stuart Drummond saw an 84th-minute header saved by Bees goalkeeper Lee Harrison.
Darren Moss then headed wide moments later before Symes struck.
Symes collectd the ball from Marc Pugh and he drilled it into the bottom corner from 12 yards.
Shrewsbury: Garner, Darren Moss, Langmead, Jones, Tierney, Wainwright (Herd 69), Drummond, Hunt, Leslie (Pugh 46), Hibbert, Nicholson (Symes 81).
Subs Not Used: Esson, Ashton.
Booked: Hunt, Hibbert, Symes.
Goals: Symes 90.
Barnet: Harrison, Devera, Yakubu, Burton, Gillet, Leary (Hendon 90), Bishop, Porter (Nicolau 83), Puncheon, Hatch, Birchall.
Subs Not Used: Beckwith, Grazioli, Norville.
Booked: Puncheon, Devera, Gillet.
Att: 5,197
Ref: Dean Whitestone (Northamptonshire).
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