Vassilis Torosidis scored Greece's winner in the 71st minute to seal their first ever World Cup victory and keep alive their chances of progressing.
Torosidis pounced after Dimitris Salpingidis's first half strike had cancelled out a Kalu Uche free kick for Nigeria, who also had Sani Kaita sent off.
"We started the game well, controlled the game, got the goal and then had a sending off. That caused us problems, especially in the first half," Nigeria coach Lars Lagerback said after the match.
"The positive thing is that if Argentina win their game we still have a chance to qualify," Lagerback said.
"We are going to take on Argentina, a world class team. They will clearly be better than us and we have got to see how to cope with them," he told reporters.
"We all know the Argentine team is of extraordinary quality."
Nigeria grabbed the lead on 16 minutes when Uche's 35 metre freekick floated past everyone including stricken goalkeeper Alexandros Tzorvas and nestled in the net.
"I couldn't see what happened from my position, what I heard they said he kicked him with the underside of his shoe. I see the Greek player laying, holding his head, so I really don't know. It looks very strange," Nigeria coach Lagerback said.
The game turned immediately in Greece's favour. Coach Otto Rehhagel replaced defensive midfielder Socratis Papastathopoulos with striker Giorgos Samaras, who minutes later had a shot cleared off the line. Then came an equaliser.
Salpingidis etched his name into Greek record books by scoring his country's first ever World Cup goal with a 44th minute strike that wickedly deflected off Nigeria midfielder Haruna Lukman before flying into the net.
