After Samaras opened his account six minutes after the break, Dons defender Jerel Ifil was sent off by referee Mike Tumilty, at the behest of his assistant James Bee, after appearing to kick out at the former Manchester City player as they clashed on the touchline.
That was a cue for a Celtic onslaught and the visitors would have been glad with the loss of only one more Samaras goal.
The win sent the Parkhead side two points clear of Old Firm rivals Rangers, who won at Falkirk earlier in the day, although the Ibrox side have a game in hand.
But on this form - three convincing home wins in eight days - Tony Mowbray's side look to have the edge as the new year looms ahead.
Artur Boruc returned to the Celtic goal for his first appearance since a Europa League game against Hamburg in October after recovering from a knee injury.
But the Poland international was a virtual spectator in a one-side affair.
The first effort on goal, though, came in the 14th minutes from former Parkhead defender Charlie Mulgrew who edged towards the Celtic box with some ease before firing wide with a right-footed shot.
That spurred the Hoops into immediate action and a surging run by Danny Fox ended with Pittodrie keeper Jamie Langfield making a fine save from the left-back's shot with Andrew Considine completing the clearance.
The game ticked along until the 28th minute when McDonald fired his angled shot from 16 yards wide of the target after being set up by Aiden McGeady, seconds before lone Dons striker Lee Miller fired a speculative dipping volley from 30 yards which went a couple of yards past Boruc's right-hand post.
In the 32nd minute Ifil came to Aberdeen's rescue when he took Samaras' pin-point cross off the toe of McDonald six yards from goal.
Then, as Celtic's pressure intensified, Considine intercepted a Samaras pass to deny McDonald from close range.
Six minutes later Langfield made another good save from McDonald but the opener was only seconds away.
In the 39th minute Andreas Hinkel picked up a Marc Crosas pass, burst in to the Aberdeen box and set up the Australia international who swept in from close range.
The Dons promised a more positive approach at the start of the second half but they were put in their place in the 51st minute when Samaras doubled Celtic's lead.
A needless foul by Aberdeen right-back Maurice Ross on Barry Robson at the corner flag had Aberdeen pressed back in their own box and when they failed to clear their lines from the Celtic midfielder's free-kick, McGeady floated a cross back in to the area and the Greece international steered his header past Langfield.
Four minutes later Samaras was involved in a controversial incident which saw Aberdeen reduced to 10 men when Ifil was shown a straight red card by referee Tumilty.
The Hoops' striker was penalised after clashing with Ifil near the touchline but, after being alerted by assistant referee Bee, Tumilty sent the Pittodrie defender off, television pictures appearing to show he had kicked out at Samaras as they untangled.
When the game restarted, Langfield had to back peddle to knock an effort from the former Manchester City striker over the bar.
As the Dons wobbled amid relentless pressure, Langfield had another save from McGeady's low drive.
Marc-Antoine Fortune replaced McDonald but it was Celtic defender Glenn Loovens who nearly grabbed a third from a Robson corner, Ross having to make a saving clearance off the line.
It was one-way traffic and in the 75th minute Samaras raced on to a McGeady pass, held off Considine all too easily before flicking the ball past the helpless Langfield.
Parkhead midfielder Landry N'Guemo then crashed a shot off the post and Samaras fired of the target from the rebound before Niall McGinn, on for McGeady, hit the upright after Crosas had put him through.
When the game ended at 3-0 the overwhelming feeling was that Mark McGhee's side had got off lightly.