Bees manager Ian Hendon handed Jake Cole a debut in goal although the on-loan QPR shot-stopper was powerless to prevent Ryan Lowe curling a shot against the top of the bar in just the tenth minute.
The home side fashioned a good chance just moments later when a long ball pumped forward was flicked on by Paul Furlong. O'Flynn raced clean through but saw his low driven attempt saved by John Danby in City's goal.
O'Flynn then saw his 20-yard free-kick in the 20th minute flash just wide of the far post, but that was it in terms of first-half chances.
The game soon picked up after the break and, within six minutes of the restart, Barnet were ahead when O'Flynn curled home a stunning 20-yard free-kick past Danby.
With Barnet now in the ascendancy, Neal Bishop fired a volley straight at Danby, before O'Flynn found the back of the net once more only for it to be ruled out for offside.
It was somewhat against the run of play when Chester levelled, Laurence Wilson and Lowe combining to set Kevin Ellison free and he made no mistake with a clinical finish past Cole.
They weren't though on level terms for long as, within ten minutes, O'Flynn converted from the penalty spot after Furlong had been brought down by Paul Linwood.
A third goal arrived 15 minutes from time when Furlong turned in Albert Adomah's cross, having initially hit the post himself.
That gave the home side some breathing space and, although Cole produced a stunning save to turn Wilson's strike onto the bar, the Bees held on for their second home win in four days.