Flynn finished off a slick move in the 27th minute following an uneventful start to the game and Falkirk comfortably held on for their first win in seven games, to pile pressure on 11th-placed Kilmarnock.
Motherwell were hit by injuries to on-loan Everton pair John Ruddy and Lukas Jutkiewicz and rarely looked like averting their second consecutive defeat despite having ample possession.
Falkirk had taken the lead in each of their previous four matches and collected just two points, but with Darren Barr back in central defence amid Brian McLean's suspension, this time they were resolute at the back.
A knee injury kept out Jutkiewicz, Motherwell's top goalscorer, and they lacked a cutting edge as they followed up the end of their unbeaten 12-match SPL run at Dundee United last week with another blow to their European hopes.
Falkirk, who brought in Kieran Duffy and the fit-again Colin Healy, began brightly on the soft surface but Motherwell threatened first when Keith Lasley's shot spooned high into the air and came down on top of the bar.
Jamie Murphy volleyed wide of the far post from 20 yards and got a brief sight of goal inside the box when Marc Twaddle slipped, but Tam Scobbie got across quickly to block his shot.
Flynn started the deciding move when he beat Tom Hateley on the left wing and played the ball inside to Healy, whose clever pass into the box found Pedro Moutinho's run.
Moutinho took out goalkeeper Ruddy with a backheel and Flynn slotted home.
Motherwell pushed forward and John Sutton headed Ross Forbes' near-post cross into the side-netting, and another Forbes cross saw Falkirk goalkeeper Robert Olejnik flapping before the visitors broke and almost doubled their lead.
Healy played another clever ball inside for Scott Arfield to run on to but Ruddy stood up to beat away the midfielder's 18-yard shot.
Scobbie then blocked efforts from Sutton and Jim O'Brien, who soon shot just over from a tight angle.
Motherwell lost Ruddy to a thigh injury at half-time and Lasley limped off just after the restart with Michael Fraser and Giles Coke entering the fray.
Falkirk saw Flynn limp off on the hour mark but they were enjoying an otherwise comfortable second period with Burton O'Brien's composure in midfield allowing them to take the sting out of Motherwell's comeback attempts.
Murphy and Sutton got shots on target but deflections took the sting out of both of them and Olejnik made comfortable saves.
Falkirk went close to a second goal when another fine passing move allowed substitute Jack Compton a chance on the edge of the box, but Fraser got down well to make a one-handed stop.
Chris Humphrey created a good chance when he got to the byline and crossed for Sutton six yards out but his header lacked conviction and failed to work Olejnik.
Barr and Scobbie continued to dominate their penalty box and Arfield should have made it 2-0 in injury-time but he shot over from eight yards after Mark Stewart had dispossessed Stevie Hammell.
Motherwell almost made him pay when Stephen Craigan flicked on a long ball for Steve Jennings but Olejnik came off his line to block as the midfielder slid in.