Lincoln 's Dany N'Guessan proved to be the most threatening player in the first half and he tested Jake Cole in the home goal early on.
Barnet responded at the other end when Paul Furlong brought out a smart stop from Robert Burch.
Overall the Imps started the brighter and went in front in the 17th minute when Aaron Brown coolly squared the ball to Michael O'Connor who had the simple task of slotting the ball home.
N'Guessan should have doubled the lead when a surging run from the halfway line resulted in him blazing the ball over, before from a Scott Kerr free-kick, Janos Kovacs saw his header well turned away by Cole.
The visitors paid for those misses seven minutes from the break when O'Flynn was left unmarked in the centre of the box to head home Yannick Bolasie's cross.
Into the second half and a mad minute on the hour mark nearly provided the third goal. Barnet spurned the first chance when Albert Adomah was clean through only to be denied by Burch, but straight from the resulting counter attack, N'Guessan should have put Lincoln ahead but he was denied by Cole.
The third goal did though arrive in the 63rd minute when Adomah this time finished off a piercing run with a finish, aided by a slight deflection, but within a minute it was 2-2 when Adrian Patulea headed home Aaron Browns' free-kick.
Both sides went for the victory in the closing stages and with just four minutes remaining, Adomah delivered a superb cross to the far post which saw John O'Flynn stoop low at the far post to head home and seal the three points.