Celtic, buoyed by Rangers' defeat at Hearts earlier in the day, sprang out of the traps and in the 27th minute the Hoops striker ran on to a Gary Hooper pass to round Dons keeper Jamie Langfield before stroking into an empty net.
The second half was less convincing and there were a couple of nervy moments for Celtic, but Stokes' strike was ultimately enough to widen the gap at the top of the table over the Ibrox men.
Under Mark McGhee, Aberdeen had suffered a club record 9-0 defeat at Celtic Park on November 6. Under new boss Craig Brown, the Pittodrie side had won four out of their last five games, but they soon found themselves under pressure.
Celtic pressed for the opener with some vigour and as the Dons rearguard defended at a stretch, Hooper's dangerous cross from the right in the 12th minute just failed to get through to his waiting strike-partner Stokes.
In the 21st minute Hoops wide man Paddy McCourt had a decent effort from the edge of the box which just flew past Langfield's right-hand post, moments before Celtic keeper Fraser Forster and stopper Daniel Majstorovic got in a tangle at the other end, almost allowing Dons debutant Nick Blackman to capitalise.
The visitors appeared to have worked their way in the game to an extent but it was Stokes who broke the deadlock after Hooper's through ball had beaten the Dons' defence,.
With the Pittodrie men looking in some hope for offside, the former Hibernian striker confidently rounded Langfield and knocked the ball in from a yard.
Referee Iain Brines incurred the wrath of the home support in the 35th when he initially gave a free-kick against Langfield in the penalty area for picking up what looked to be an Andrew Considine pass back before changing his mind under duress from the Pittodrie players.
But the Celtic players refused to be distracted and in a swift breakaway five minutes from the interval, Stokes sent Hooper racing down the right and was in the box to take the return ball.
However, Langfield was equal to the Irishman's drive from 12 yards, pushing the ball over for a corner which came to nothing although there was still plenty of defending to be done by Brown's men before half-time.
Aberdeen might have taken some comfort from the occasional moments of nervousness in the Celtic defence which caused some concern for the home fans in the first half.
However, the Granite City club were put on the back foot again almost immediately after the game restarted although in the 50th minute Dons striker Chris Maguire had a snap-shot from 25 yards which went past the far post.
Moments later, after Hoops defender Thomas Rogne failed to control a long ball, Maguire came closer with a better effort from the same distance.
As Celtic reasserted themselves and the Dons retreated, McCourt and skipper Scott Brown both had rather poor attempts from distance.
The play stuttered rather than flowed towards the Aberdeen goal
but Celtic could not get the second goal which would have made the latter stages less nervy.
In the 75th minute former Arsenal star Freddie Ljungberg was given a huge cheer when he replaced McCourt to make his home debut.
Play was stretched in the closing minutes but Celtic held on against a late Aberdeen surge to take the points and increase the pressure on Old Firm rivals Rangers as the SPL title races hots up further.