In a lively opening 45 minutes the visitors forged into a two-goal lead, who despite a spirited second-half surge by the Dons, held on to win.
It was the home side who came closest to opening the scoring after ten minutes.
From a Barry Nicholson corner Alexander Diamond rose above Mark Reynolds to bullet in a powerful header which was cleared off the line by Steven McGarry.
In the following minute an excellent reverse pass from Scott Severin picked out Lee Miller, his first-time effort was driven into the ground and only an acrobatic save by Graeme Smith, who finger-tipped the ball over the crossbar, saved Well.
Motherwell were always a threat and after 14 minutes a weak clearance from Jackie McNamara fell to the edge of the area where Stephen Hughes crashed a fierce shot just wide of the upright.
In 20 minutes clever improvisation from Hughes saw his clipped shot almost surprise Derek Soutar, with the Dons keeper back-tracking to tip the ball over the bar.
Aberdeen came close again after 26 minutes when Richie Foster's long ball out of defence found the head of Miller, he picked out Steve Lovell, who turned his marker before crashing in a great shot which flew just wide of the far post.
Aberdeen had upped the tempo of the game and in quick succession passed up two great chances. Firstly Nicholson failed to hit the target from eight yards with a goal at his mercy, this was followed minutes later by Jamie Smith, whose crisp effort from 12 yards was brilliantly held by Graeme Smith.
The visitors shocked the home side after 34 minutes when Ross McCormack played the ball back into the path of Paul Quinn, whose low effort from 22 yards gave Soutar no chance.
Back came Aberdeen again but Graeme Smith stood up brilliantly to hold a sharp Nicholson effort.
Aberdeen were rocked after 37 minutes when Chris Porter rolled free of his marker and onto a Phil O'Donnell through ball. The big striker showed good composure as he stroked the ball past Soutar to make it 2-0.
The Dons continued to create chances but Miller and Lovell both passed up decent opportunities as the game moved towards half-time.
On 48 minutes a neat cushioned pass from Severin found Lovell and he should have brought his side back into the game, but yet again Graeme Smith was the equal of the big striker, getting down smartly to save.
Aberdeen gave themselves a lifeline on 65 minutes when a sublime free-kick from Jamie Smith went up and over Motherwell's defensive wall and beyond the reach of Graeme Smith and into the top corner of the net.
Aberdeen boss Jimmy Calderwood threw on additional strikers for his side to go for an adventurous 3-4-3 formation.
However, his side lacked composure to create any further meaningful chances as Motherwell ran down the clock to fully deserve their win and three valuable points.