After a fairly uneventful 15 minutes, Aberdeen came close to scoring when Scott Severin headed the ball into the path of Barry Nicholson, but his crisply hit shot from 24 yards flew just wide of the upright.
The home side upped the tempo but, despite plenty of endeavour, failed to create any meaningful chances.
Aberdeen deservedly took the lead on 28 minutes. Alexander Diamond climbed above Stephen Craigan to head the ball home off the underside of the crossbar from a Jeffrey de Visscher corner.
In the 39th minute indecision in the Well defence saw the ball break to Steve Lovell but, from a good position on the byline the striker failed to pick out Darren Mackie with the goal at their mercy.
Alan Maybury was getting into great positions as he played like a winger at times. From his cross late in the half Nicholson was unlucky to see his header fly just over the ball.
Aberdeen passed up a great opportunity to extend their lead in the 50th minute. A clever de Visscher ball saw Mackie race away from Mark Reynolds only to shoot weakly into the arms of visiting keeper Graeme Smith.
A snap-shot from the impressive Maybury brought a brilliant fingertip save from Graeme Smith as the Dons began to turn the screw.
Diamond went close to adding his second goal of the evening when he got the slightest of touches to head the ball just the wrong side of the upright from another well delivered de Vischer free-kick.
Motherwell ought to have been on level terms minutes later. A long throw from Craigan caused panic in the Dons defence, Chris Porter heading the ball on only for David Clarkson to somehow scoop his effort over from five yards.
The visitors sensed they could get something from the match and were awarded a spot-kick on 80 minutes.
Diamond needlessly upended Porter on the edge of the area leaving referee Douglas McDonald with an easy decision. The big striker dusted himself down before stepping up to fire the ball to Derek Soutar's left only for the keeper to fingertip the ball away.
The visitors were not to be denied however and with eight minutes remaining deservedly drew level. A second-half substitute, Darren Smith , fired a great shot home from the 20-yard mark, through a ruck of players and into the corner of the net.