Longford had the better chances in the first period.
First, David O’Sullivan headed wide from a pinpoint cross from Don Cowan in the 32nd minute.
O’Sullivan went close again a minute later when he flashed a shot just over.
Harps lived dangerously in the early stages of the second period and were lucky not to go behind in the 52nd minute when Flynn headed wide from a superb cross from Salmon.
They eventually did concede when Glen O’Connor fired home a cracking free kick in the 85th minute.
Harps manager Ollie Horgan replaced Caoimhin Bonner and Josh Mailey with Gareth Harkin and Darah Black for the last five minutes in a desperate attempt to grab an equaliser but Longford held on to leave Ballybofey with all three points.
There was a minute’s applause before the kick-off for Oisin Merritt, the young Harps reserves player who is critically ill in a Spanish hospital following a fall in the early hours of Monday morning last.
Finn Harps: Conor Winn, Caoimhin Bonner (Gareth Harkin 87), Ciaran Coll, Keith Cowan, Damien McNulty, Michael Funston, Josh Mailey (Darah Black 87), Pat McCann, Ruairi Keating, Kevin McHugh.
Unused substitutes: Graham Fisher, Mark Forker, Paul McVeigh, Shaun Patton, Carel Tiofack.
Longford Town: Paul Hunt, James Mulhall, Pat Flynn, Pat Sullivan, Willie Tyrell (Glen O’Connor 34), Kevin O’Connor, Don Cowan (Peter Hynes 68), Stephen Rice, Mark Salmon, David O’Sullivan, Gary Shaw.
Unused substitutes: Conor O’Brien, Noel Haverty, Chris Bennion, Sean Russell, Lorcan Shannon.
Referee: Ben Connolly.