Pat Fenlon's away side had gone close in the first half through Byrne and through namesake Stuart who headed wide of Gary Rogers' goal in the 43rd minute.
Gary Cronin went closest for Paul Doolin's new outfit, before ten minutes after the break, Byrne was played through on Rogers by U21 international Wesley Hoolahan, and he made no mistake, poking the ball past the United goalkeeper from eighteen yards.
The game also marked Shelbourne's first clean sheet in the league since the end of July, and a timely boost ahead of two Dublin derbies in the next week, at home to St Pat's on Friday night, and Bohemians away on Monday.
LONGFORD TOWN 0 CORK CITY 1 (O'Callaghan 88 pen)
A well-struck penalty two minutes from time was enough for Cork City to rescue the points at Flancare Park last night, and score their first away win since April in the league.
Playmaker George O'Callaghan, deputising for the injured John O'Flynn, up front in tandem with Kevin Doyle, slotted home the all important spot kick to edge Pat Dolan's men three points behind third-placed St Pat's.
In a sporting gesture, O'Callaghan unveiled a t-shirt proclaiming ' Top gun, John O'Flynn, played 45, scored 30, to be continued...', when celebrating his goal.
U21 international O'Flynn has been sidelined since being stretchered off in a 1-1 away draw with UCD in early September. A scan last week revealed that the striker will be out of action for four to six weeks, severely denting City's league and European aspirations.
Their next game has been switched from Friday to Saturday night, against Shamrock Rovers at Turner's Cross. Due to crowd trouble at Rovers' Dublin games, the switch has been ordered, although the Leeside game is officially a 'Shamrock Rovers' home game'.