Needing a win to qualify in Fortaleza on Tuesday, Greece left it late, with Samaras' 93rd-minute spot-kick sealing their progression from Group C in dramatic circumstances.
The penalty was given after the forward was tripped by Giovanni Sio and the Celtic man dusted himself down before scoring to Boubacar Barry's left.
Greece had initially taken the lead through Andreas Samaris – an early replacement for the injured Panagiotis Kone – in the 42nd minute.
Greece's start was thrown into disarray by two forced substitutions inside the first 30 minutes, as Kone and goalkeeper Orestis Karnezis suffered injuries.
But they almost took the lead in the 33rd minute from a quick break, as Holebas – played in following Samaras' well-weighted through-ball – saw his fierce strike come back off the crossbar.
Greece's threat on the counter only grew as the second half progressed and Ivory Coast were rescued by the bar for a second time with 22 minutes to go, when captain Karagounis tried his luck from 35 yards.
The introduction of Bony gave Ivory Coast another dimension and after wasting a pair of half-chances, the Swansea City forward drew his side level, producing a composed first-time finish after Gervinho's clever cut-back.
But it was the Greeks who looked more likely to score the winner, as Dimitrios Salpingidis flashed an effort wide, before Sio's foul gave Samaras the chance to be a hero.
And it was an opportunity he took with both hands, slotting past Barry to earn Fernando Santos' side a place in the next round.
