The Dark Blues forward struck ten minutes after Noel Whelan seemingly put the Dons on their way to victory.
Aberdeen boss Jimmy Calderwood was forced to make two changes to his side with Alexander Diamond suspended and Richie Byrne missing out of because of a virus.
On the plus side for the Dons both Markus Heikkinen and Phil McGuire were both fit enough to start the match as the home side tried to make it five SPL victories in a row for the first time this season.
Dundee boss Jim Duffy brought his side north knowing it had been 12 years since the Dark Blues had tasted defeat in the Granite City. But the visitors' chances of the keeping the run going were dealt a blow when Steve Lovell failed a fitness test ahead of the game.
Both sides made a bright start with some neat passing football on show. The first real chance came after seven minutes when a Steven Robb cross picked out Garry Brady inside the area, he controlled it before seeing his shot held well by Ryan Esson.
The Dons' first chance came two minutes later when Whelan fired in a low volley from the edge of the area but Derek Soutar dropped down low to his right to hold the big striker's effort.
After 38 minutes the home side almost took the lead when Darren Mackie played the ball into the path of Kevin McNaughton 25 yards from goal and his effort went over the head of Soutar, but came back off the face of the bar.
In the 55th minute the home side again tested Soutar from distance. Chris Clark picked the ball up 25 yards from goal before firing in a powerful left-foot shot that the goalkeeper gathered at the second attempt.
The opening goal came after 63 minutes courtesy of a wonderful piece of skill from Whelan, who collected the ball almost 30 yards out. He looked up and saw Soutar off his line and sent the most delightful of shots over the head of the keeper and into the top left-hand corner of the net.
Four minutes later Dundee almost carved out an equaliser when a Robb cross saw Robert Mann beat Esson to the ball to head goalwards, but Jamie Winter was on hand to clear the ball off the line.
Dundee were back on level terms after 73 minutes when a free-kick from just inside their own half was flicked by John Sutton. It went through to McManus, who looked suspiciously offside, but he did not wait around to see the assistant referee's flag and neatly tucked the ball beyond Esson.
That was the queue for an onslaught from the home side, who pinned Dundee back in their own half and created several good scoring opportunities, the best of which came when Scott Severin popped up 25 yards from goal to send a low right-foot drive inches wide of the post.
In the dying moments of the game Aberdeen again pushed for a winner as John Stewart's long ball found McNaughton, who cut the ball back across the face of goal but Brent Sancho got in ahead of Mackie to clear the danger.