O'Flynn opened the scoring after 11 minutes when Aaron Dawson's low cross from the right was knocked on by Sam Parkin and O'Flynn fired home a low shot from the edge of the penalty area which took a slight deflection on its way in.
O'Flynn should have doubled Exeter's lead after latching onto a poor back pass, but after rounding Ross Worner, he failed to get decent contact and rushed the chance with the goal gaping.
However, he made amends after 36 minutes when he finished off a brilliant and incisive counter-attack. It started with a quick throw by goalkeeper Artur Krysiak to Dave Wheeler, who sprinted down the right wing and crossed for O'Flynn to finish from close range.
The second half was a more even contest although chances were at a premium. Arron Davies was denied by Worner while Wimbledon's best opening fell to Andy Frampton but his header was cleared off the line by Craig Woodman.