Chris Humphrey inspired the hosts to their second win over the Dons since former manager Craig Brown's departure for Pittodrie.
Humphrey blasted home inside 15 minutes and set up several more chances before Shaun Hutchinson looked to have made the points safe in the 87th minute.
Nikola Vujadinovic headed Aberdeen back into it in injury-time but Motherwell held on to move nine points above the Dons.
Just like they had done during their 3-0 midweek Scottish Cup win over Dundee United, Motherwell made a bright start and Humphrey got past Steven Smith in the first minute before sending in a cross that Keith Lasley eventually sent wide.
Steve Jones, in for the injured Francis Jeffers, earned space to shoot over before Jamie Murphy came closer when he beat two men and played a one-two with Lasley before curling inches wide.
The home side took the lead after Humphrey's pace proved too much for Smith. Motherwell won the ball in midfield and Lasley played it over Smith's head for Humphrey to chase. The winger made up about five yards and got away from the left-back before thumping the bouncing ball into the top corner from 16 yards.
Motherwell, with Maurice Ross making his debut at right-back, sat back in the aftermath of taking the lead but Aberdeen, who were without the suspended Zander Diamond and injured pair Ryan Jack and Paul Hartley, were unable to put them under any pressure with Nick Blackman getting little joy from his former team-mates, or supporters.
Chris Maguire volleyed wide from a difficult chance two minutes after the restart as Motherwell made a slow start to the second half.
But Motherwell soon picked up and Jones should have put them two ahead only to slice the ball well over from four yards out after Humphrey had curled a cross in between Aberdeen goalkeeper Jamie Langfield and his defenders.
Sone Aluko had a brief sight of goal after a one-two with Blackman but Stevie Hammell got back to snuff out the danger.
Aberdeen had a great chance on the hour mark after Vujadinovic played Maguire through but Darren Randolph got down brilliantly to push the striker's attempted finish past the post.
Randolph then held Andrew Considine's header after Derek Young sent the ball back into the box following a corner.
Aberdeen, with Josh Magennis on to give them a quartet of attackers, were looking far more dangerous and the substitute headed straight at Randolph following Rob Milsom's free-kick.
But Humphrey again caused problems when he raced past Considine, who had been booked moments earlier for a foul on the winger, and crossed for substitute Bob McHugh, whose sliding effort was diverted wide.
Motherwell brought on defender Stephen Craigan for Murphy and soon lost Gunning to a shoulder injury after he fell heavily following a foul by Aberdeen substitute Peter Pawlett.
Lasley soon took a knock and struggled on with no substitutes left but Motherwell came close when Humphrey set up McHugh, only for Langfield to make a diving one-handed stop.
But Hutchinson raced in to force Tom Hateley's inswinging corner home from close range to cue widespread taunting of Brown among the home fans.
They were soon silenced when Vujadinovic headed home Maguire's cross in the second of five minutes of injury-time and almost saw two points slip away in the dying seconds when Rory McArdle headed Maguire's corner against the post, but Steven McLean blew for a foul and soon time was up.