A dour battle at Pittodrie was drifting to a goalless draw until a moment of sheer brilliance from Flood broke the deadlock just three minutes from time.
The Hibs defence had weathered some late pressure from the hosts before Flood picked up a poor clearance and hammered an unstoppable 25-yard piledriver beyond Ben Williams and into the far corner.
Chances were at a premium from the outset, although Hibs had early penalty claims waved away after Paul Heffernan fell under a challenge from Jamie Langfield after an error of judgement by Mark Reynolds.
The Dons were also denied a penalty midway through the first half when Michael Nelson appeared to handle a cross from Peter Pawlett, but referee Craig Thomson was unmoved.
Williams did well to keep out a decent effort from Reynolds as the home side stamped their authority on the game, but they almost went into the interval a goal down as Heffernan pulled his shot wide after latching onto a woeful pass from Jonny Hayes.
Niall McGinn flashed a low shot wide of the target, while Langfield comfortably dealt with a long-range free-kick from Paul Cairney.
McGinn headed wide at the other end, but Flood's magnificent strike ensured Hibs left empty-handed as Aberdeen moved within 10 points of leaders Celtic.