Aberdeen, with five player chosen for the Scotland A and B squads, were without suspended defender Ilian Kiriakov.
In the opening minutes both teams forced corners but neither was converted. Thereafter the game developed into a midfield struggle for supremancy by both sides. David Rowson headed visiting Aberdeen into the lead at East End after 19 minutes. Eion Jess delivered a cross despite a strong challenge from defender Andy Tod, Rowson hit the back of the net.
Dunfermline then twice forced two quick corners but could not penetrate a tight Aberdeen defence in front of their goal.
In the 35th minute Hamish French was booked for a handball offence as he stretched to connect with a clever Dave Bingham forward pass inside the penelty box.
Four minutes later Billy Dodds was given the ball with a clear shot at goals but he pulled it to rebound off a defender.
The half ended with the Pars fighting hard to gain an edge over a confident Aberdeen side.
Dunfermline looked set for three points when they took the lead in the 53rd minute. Andy Smith knocked a pass down to Hamish French who slipped the ball to Andy Tod who in turn rifled home his second goal from seven yards.
For the next 10 minutes Dunfermline were on top with Aberdeen scrambling to regain their form.
In the 64th minute the visitors equalised when a punch out from keeper Westwater landed at Davis Rowson's feet and he shot perfectly into the corner of the net.
The six minutes later Brian O'Neil put Aberdeen ahead.
Aberdeen manager Alex Miller was left rueing the loss of two points after the 3-3 thriller at Dunfermline.
Miller said: "When you score three goals away from home you expect to get three points but we threw the points away with bad defending.
"We should have finished Dunfermline off in the first half."
DUnfermline manager Bert Paton said: "It was good to get three goals but I wa annoyed at some of our defending. We now have a young defence, all in the early 20's and they need a bit more experience.
"We have now gone six games with only one defeat and are taking ourselves further away from the possibility of relegation."