Steve Crawford and Scott Severin ensured that Dunfermline endured more misery at the bottom of the SPL.
Two goals in a 10-minute spell late in the first half were enough to settle the issue and give Aberdeen all three points.
To add to the gloom at East End Park, Lee Makel missed a second-half penalty which at least would have given the Pars their first home goal.
Dunfermline should have scored after 13 minutes. Yannick Zambernardi provided the most inviting of crossed for Mark Burchill, but he somehow brushed a header wide from only six yards.
Jamie Smith then created a shooting chance for Aberdeen after beating Darren Young, but his 20-yard effort was always curling high and wide.
Smith had the Pars defence in turmoil with another great run into the penalty box, but he was crowded out and Jamie McCunnie prevented his final pass reaching Crawford.
Four minutes later, Crawford had the first shot on target after a patiently-built attack gave Barry Nicholson the chance to set up his front man. McGregor failed to hold the ball but recovered to snatch the ball away from Steve Lovell.
The Dons snatched the lead 10 minutes from the break. Nicholson picked out Crawford again and he hooked a right-foot shot high into the net past Allan McGregor.
Aberdeen grew in confidence after the goal, and McGregor did well to turn a Kevin McNaughton shot past his post as they threatened a second.
It came on the stroke of half-time as Smith played in a free-kick and Severin nipped in front of his marker to nod the ball home.
Dunfermline went to three at the back in the second half and pushed McCunnie forward and there was a better balance to their play.
They were awarded a soft penalty after 54 minutes when a cross from substitute Bartosz Tarachulski struck Alex Diamond's arm, but Makel's spot-kick struck the post.
Aberdeen almost snatched a third 13 minutes from time when Crawford laid the ball back to Smith, but his shot was a yard wide