Samaras was adjudged to have been brought down by substitute Giovanni Sio and the former Manchester City and Celtic winger calmly slotted in from the spot for the win that puts Greece through to the knockout stage.
Ivory Coast would have advanced with a draw.
Substitute Wilfried Bony had equalised for Ivory Coast in the 74th, beating goalkeeper Pangiotis Glykos from close range after being set up by Gervinho.
The Greeks had taken the lead just before half-time through substitute Andreas Samaris.
Veteran striker Didier Drogba started for Ivory Coast along with Yaya and Kolo Toure despite the recent death of their brother Ibrahim. The Ivorians wore black armbands as a sign of mourning.
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