The Dons recovered from Henri Anier's first-minute opener to claim their first league win over Well in almost five years, McGinn's spot-kick successes (62 & 84) sandwiched by a goal from Mark Reynolds against his former club.
Motherwell were lacklustre for long spells just days after their Europa League exit in Russia but fans were hopeful of domestic tonic when Anier raced onto John Sutton's through-ball and finished with just 40 seconds gone.
Aberdeen had chances to draw swiftly level but were twice denied by the crossbar before the break, Peter Pawlett and then Calvin Zola - after a neat sidestep gave Stephen McManus the slip - thwarted.
Zola's task soon after the restart, when Willo Flood had cleverly set him up, seemed far easier but the former Burton man swiped at air and Aberdeen must have thought this was one of those days.
A deserved equaliser finally came shortly after the hour when Jonny Hayes drew a foul from McManus, McGinn accepting the chance and finding the top corner.
Aberdeen continued to carry a threat and took the lead when Reynolds evaded his marker to convert a Hayes free-kick (76), McManus penalised this time for a push on Josh Magennis.
Lee Hollis made a fine save with his feet to deny Magennis but a third goal did come when referee John Beaton spotted a foul on Joe Shaughnessy from the resulting corner, McGinn finding the same corner to cap what turned out to be a comfortable win.