Friday's clash at Pittodrie seemed destined for a scoreless draw after 86 minutes devoid of clear-cut chances, but the former Celtic man's screamer was enough to consign Hibs to a first defeat in six league outings.
Both sides saw penalty appeals turned down by referee Craig Thomson, after Paul Heffernan was felled by home goalkeeper Jamie Langfield in the opening exchanges and Michael Nelson appeared to block Peter Pawlett's cross with his hand 27 minutes in.
The visitors should have opened the scoring a minute before the interval, but Heffernan scuffed wide after Aberdeen winger Jonny Hayes made a mess of his clearance.
A dour second half offered little in the way of entertainment, Heffernan barely testing Langfield with a 20-yard effort, while the hosts struggled to deliver a telling final ball.
However, a moment of magic secured all three points as Flood plucked the ball from the air in the left channel before drilling a wondrous effort across Ben Williams and into the corner from 30 yards.
Second-placed Aberdeen are now 10 points behind runaway leaders Celtic, while Hibs remain sixth.
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