The Greek striker stepped off of the bench to help the home side claim an astounding victory after going 3-1 down to prevent a third straight defeats for the Bhoys
Kris Commons had put the Parkhead side into the lead before a Scott Vernon strike and a Josh Magennis double had the Dons in a commanding position, but Charlie Mulgrew and Gary Hooper helped the hosts back into the game before Samaras sent the home crowd into ecstasy with a late winner.
Neil Lennon made three changes from the side that went down to a shock defeat away to Ross County last Saturday, with Remi Gershon, Dylan McGeouch and Miku all dropping out to be replaced by Mikael Lustig, Emilio Izaguirre and Commons.
Craig Brown - who had announced he would be retiring as Aberdeen manager at the end of the season - made only the one change, with Clark Robertson out injured and Magennis replacing him.
Celtic opened the scoring within the first 12 seconds, as a long ball from kick-off found Gary Hooper who played in Anthony Stokes. He then drifted the ball to the left hand side of the box for Commons, who rifled a shot under Jamie Langfield.
With less than a minute to go in the half the Pittodrie side got level, as Magennis beat Kelvin Wilson to a long ball inside the box and cut it back for Vernon to slam into an empty net.
The visitors took the lead with eight minutes played in the second half as they cut the Celtic defence open with a counter attack, which saw Gavin Rae feed Magennis on the left-hand side of the box to place the ball under Fraser Forster.
Langfield almost gave the home side an equaliser as Commons twisted and turned on the edge of the area before unleashing a strike which the Dons stopper fumbled, but managed to gather at the second attempt before Hooper was able to finish.
On the hour mark the visitors scored their third after Celtic had failed to clear a corner from the left; the ball ended up with Rae who curled a 25-yard strike towards goal, which was flicked into the net by Magennis for his second of the game.
Celtic got one back eight minutes later after a corner from the right by Commons pinballed around the area before arriving at the feet of Mulgrew, whose low strike deflected off a couple of defenders and into the roof of the net.
With less than five minutes remaining in the game the home side got back on level terms as Aberdeen failed to clear yet another corner from the left, and Hooper managed to knock it home from less than a yard out.
Deep into injury-time Celtic claimed the victory after Russell Anderson brought down Hooper on the edge of the area, Commons whipped the free kick into the box and Samaras somehow managed to find the net to claim an improbable victory.