The Greece international was brought off the bench at half-time and responded by scoring City's two goals as they have suddenly become one of the Premiership's form teams.
Samaras had had a torrid start to the season scoring only three times before finally producing the sort of form which prompted Pearce to pay £6million for him 12 months ago.
He struck within five minutes of his introduction with a goal he started and executed superbly and then sealed victory from the penalty spot.
But Everton showed great resilience as they refused to throw in the towel and produced a sterling fightback.
Substitute Victor Anichebe was denied by a superb save from keeper Nick Weaver before Leon Osman halved the deficit with little over six minutes left to set up a frantic finish to a match which had been flat after a lifeless opening period.
City had one enforced change from Saturday's win at West Ham as Stephen Ireland was ruled out through an ankle injury.
Ireland's place went to DaMarcus Beasley, the substitute who scored the match-winning goal at Upton Park in what was a straight swap in the centre of midfield.
Everton, who had beaten Newcastle 3-0 on Saturday, brought in Simon Davies and James Beattie as Andy Van der Meyde and Anichebe stood down.
In an appalling opening half, neither goalkeeper had a shot to save. Andy Johnson fired narrowly wide inside the opening half-minute but, sadly, it was not a sign of things to come.
Joseph Yobo saw a header fly just wide while Davies shot well wide and Beattie flashed a header well off the mark.
City, again playing a 3-5-2 system, had to wait an astonishing 33 minutes before having their first shot at goal.
And it was hardly worth the wait as Micah Richards ' long-range drive finished nearer the corner flag than the goal.
City's best chance of the opening period came in the 42nd minute when Bernardo Corradi 's close-range shot was blocked by Joleon Lescott with City's claim for a handball rejected by referee Uriah Rennie.
And, in stoppage time, Darius Vassell shot narrowly wide though keeper Tim Howard had his shot well covered.
City made a half-time change bringing on Samaras for the ineffective Corradi and also significantly changing to a 4-4-2 line-up.
And City finally broke the deadlock within five minutes of the re-start when Samaras started and finished a stunning move.
Samaras made a powerful run from his own half, released Beasley on the left and then ran in to meet the American's low cross with a neat, near-post shot.
And City might have doubled their lead not long after when Richards' long-range drive was well kept out by Howard, diving low to his right.
Samaras, lifted by a rare goal for City, forced Howard into a diving save with a drive from 25 yards.
Rejuvenated City sealed victory in the 72nd minute when Vassell burst through on goal only to be brought down by Howard with Samaras scored from the penalty spot.
But there was almost a final twist as Everton mounted an unexpected comeback which so nearly earned a point. Anichebe was denied by a superb save from Weaver low to his left.
And the value of that save was reinforced when Everton found the net with little over six minutes left as Phil Neville crossed from the right and Osman shot high into the roof of the net from 10 yards as Weaver was finally beaten.