The Greece striker headed the home side into the lead in first-half added time and scored his second with a fine drive seven minutes after the break to make it eight SPL wins in a row for Neil Lennon's men.
Killie substitute Danny Racchi fired in a consolation goal with three minutes remaining but with Rangers losing at St Mirren, the Hoops now have a chance to go top of the table going into 2012.
After being 15 points behind the champions at one stage - albeit with two games in hand - the ascendancy is with Celtic who must feel they are coming to form at the right time.
While the result in Paisley was something of a shock, there was little surprise about the outcome at Celtic Park.
Kilmarnock had not won at Celtic Park in 56 years while the home side, who had Joe Ledley in for injured Daniel Majstorovic, were looking to continue their fine domestic form
The visitors could have been excused for fearing the worst but they lined up in a positive shape with Dean Shiels supporting Paul Heffernan and Gary Harkins.
Manager Kenny Shiels had made three changes with James Fowler, back from suspension, Mohamadou Sissoko and Danny Buijs coming in for Alex Pursehouse, Zdenek Kroca and James Dayton and his side impressed in an entertaining first half.
Celtic had to so some defending in the early stages although in the ninth minute Hoops midfielder James Forrest sent a speculative 30-yard drive just past Cameron Bell's left-hand post.
Moments later, in an impressive Killie move, Heffernan set up Shiels and the Irishman's low drive from 16 yards sped past Fraser Forster but also beyond the Celtic keeper's left post.
The Parkhead men had a great chance in the 14th minute when Forrest's low drive was spilled by Bell but Gary Hooper chipped the rebound over the bar, before Shiels had another effort saved by Forster at the other end.
Shiels ended another Rugby Park threat by blasting a shot over the bar from the edge of the box, more evidence that the Ayrshire men had not travelled with a point in mind.
An entertaining game began to heat up. Celtic midfielder Beram Kayal was booked for tripping Shiels before Killie skipper Manuel Pascali was yellow-carded for a late challenge on Ledley.
Celtic were making hard work of it. In the 33rd minute skipper Scott Brown had a left-footed shot easily saved by Bell, one of the few times the ball got past the resolute Killie defence.
However, all Kilmarnock's good work was undone as the game entered added time.
Celtic's tireless right-back Cha Du-ri raced to the byline and managed to send in a looping cross which was headed past Bell by Samaras and the Greece international had the cheers of the relieved home fans still ringing in his ears as he ran up the tunnel at the break.
There was a claim for a Killie penalty three minutes into the second-half when Forrest blocked Buijs's attempted cross but referee George Salmond kept his hands at his side.
Forrest was replaced by Kelvin Wilson moments later and the former Nottingham Forest defender went to centre-back alongside Victor Wanyama, with Charlie Mulgrew moving to left-back and Ledley moving up one.
Much of the Celtic fans' attention, though, was on the game at St Mirren and there was a huge cheer when news of the Buddies' victory over Rangers was confirmed.
The home side took inspiration from the shock result and in 52nd minute Samaras took a Hooper pass and swerved his way into the box before slamming a low drive past Bell.
The big striker looked to have all but sealed the win and he was given a standing ovation in the 65th minute when he was replaced by Mo Bangura.
Killie were more or less reduced to keeping Celtic at bay while the home support chanted 'bring on the Rangers'.
Another good run down the right by Cha in the 72nd minute ended with the full-back crossing perfectly to Ki Sung-yueng but his fellow South Korean mis-kicked with his volley from 12 yards and an increasingly bedraggled looking Killie side escaped punishment.
In the 87th minute Killie substitute Racchi, on for Shiels, rifled in a shot from 25 yards which beat Forster to make it a nervy ending with Wanyama blocking a goal-bound shot by Harkins moments later, with Forster out of his goal.
However, there was to be no undeserved equaliser and the cheers at full-time indicated that the Celtic supporters rightly fancy their chances against their city rivals in midweek.