McGinn opened the scoring in the 14th minute when he collected Ryan Jack's cushioned header and curled a left-foot shot over Hibs goalkeeper Ben Williams from 25 yards out for his 11th goal of the season.
The 26-year-old Northern Ireland international striker then made it 2-0 in the 62nd minute when he crashed the ball home off the underside of the crossbar from just inside the area after Adam Rooney had centred from the right.
McGinn also struck the post with a curling left-foot effort in the 40th minute, three minutes before Rooney rattled the upright with a cushioned volley from Barry Robson's cross.
Hibs enjoyed a dominant spell after McGinn's opener as Paul Cairney and James Collins had shots blocked, while Sam Stanton also saw an effort cleared.
The hosts had appeals for a penalty waved away in the second half when Collins tumbled in the area under Russell Anderson's challenge shortly before McGinn's second goal.
Tom Taiwo failed to connect properly when presented with a chance to put Hibs back in the game with 20 minutes remaining and Stanton then fired wide following a mazy run.
However, Aberdeen held firm in the closing stages for a confidence-boosting victory ahead of Sunday's Scottish Cup semi-final against St Johnstone.
Hibernian, meanwhile, remain only four points clear of 11th-placed Partick Thistle with five matches left after the split, and they have now gone eight games without a win, losing their last four.