David Goodwillie was denied by the crossbar early on in what proved to be a tightly contested first half.
The home side increased the pressure after the break though, and had the breakthrough in the 69th minute when Peter Pawlett pounced on Jonny Hayes's rebounded effort.
Derek McInnes' side secured a sixth victory in seven games to close within four points of Celtic, while Kilmarnock's winless run now stands at eight matches.
A fast-paced start from the visitors saw Martin Canning leap highest to power home a header from Ali Crawford's corner.
Elsewhere, Brian Graham's 62nd minute penalty was enough to seal a 1-0 win for St Johnstone at home to 10-man Inverness Caledonian Thistle, who saw Ross Draper was given his marching orders for catching Simon Lappin with a stray elbow.
St Mirren also had to play with 10 men, Steven Thompson's first-half dismissal hampering them as they went down 1-0 to Motherwell.
