The Imps were desperate for three points after losing their last two home games. They almost went in front after 18 minutes when a corner from Lee Frecklington found the head of Adie Moses but the centre-back's effort was cleared off the line by Andy Hessenthaler.
Three minutes later Dany N'Guessan rose above the Barnet defence to meet a free-kick from Jeff Hughes but his header flew over the bar.
Barnet began finding holes in the Lincoln defence early in the second half. Ismail Yakubu had a shot blocked, and then Adam Birchall fired over from outside the box.
But Lincoln grabbed what proved to be the winner in the 51st minute. Frecklington burst into the box and held off three defenders before firing into the top corner for his 10th goal of the season.
Six minutes later Barnet almost drew level when a mistake by Nat Brown let in Oliver Allen. The former Birmingham City striker spotted keeper Alan Marriott off his line and lobbed in a shot from 25 yards, only to see Marriott reach back to make a spectacular save.
Birchall then set up Dean Sinclair but from close range the midfielder shot straight at Marriott.
Barnet continued to create chances and a mistake by Moses set up Jason Puncheon but the talented youngster shot over. And Puncheon wasted two more good openings as Lincoln struggled to hold on to their lead.
But City should have made the game safe in the 88th minute when substitute Spencer Weir-Daley somehow headed over with the goal at his mercy.
Late in stoppage time, Paul Mayo made a dreadful mistake to send Puncheon clear again. The winger found Birchall with his pass but the striker shot wide when it looked easier to score.