The 2012 co-hosts and competition rookies secured their passage to the last eight with a 2-1 win over the Group A favourites at a rain-sodden pitch in Bata. An astonishing achievement for a side rated 151 in the FIFA/Coca-Cola World Ranking.
And they did it the hard way, Iban 'Randy' Iyanga putting them into a 62nd minute lead only for Moussa Sow to level a minute from time.
But David Alvarez hit back in the fourth minute of injury time to create history for this central west African nation. Alvarez burst into tears when the final whistle sounded as the crowd went berserk.
Their achievement was all the more notable considering teams of the calibre of Egypt, winners in 2006, 2008, and 2010, Cameroon, Nigeria, South Africa and Nigeria couldn't even make it through qualifying.
For Senegal the result spelled an embarrassing early flight home, this defeat coming on the back of their opening 2-1 loss to Zambia combined with the Zambians' 2-2 draw with Libya in the other Group A match.
Victorious captain Juvenal said: "We were a little lucky to score the second goal in the last few seconds! It's fantastic for us and our supporters. We're very hopeful for the future. Now we want to beat Zambia in our last match because we want to finish top of the group."
Senegal coach Amara Traore commented: "I congratulate Equatorial Guinea for qualifying. As for us, we tried everything, I'm content for my players, they gave their all. I am frustrated though, as we came here to make an impact."
Glory for Equatorial Guinea has swelled their bank balances too. They picked up a USD $1 million bonus from the son of the country's president for Monday's 1-0 defeat of Libya, with another bonus on its way for their heroics against Senegal.
Libya stay afloat in the wet
Zambia's match against Libya was preceded by a deluge which rendered the pitch virtually unplayable. Ahmed Osman struck early in each half for the Libyans but his goals were cancelled out as Emmanuel Mayuka and captain Christopher Katongo netted.
Libya, whose players risked their lives to fulfil qualifying fixtures while a civil war raged in the north African country, retain a mathematical chance of making the last eight.
The kick-off was delayed 76 minutes after torrential late-afternoon rain dotted the pitch at the 35,000-seat stadium with mini lakes. Efforts to clear puddles of varying sizes included the use of brooms, long and short planks of wood and the belated appearance of a machine which speeded up the process.
Katongo questioned the decision to stage the game. "It wasn't easy and I'm quite disappointed the referee took this decision. It was only in the middle of the pitch that we could play a bit, everywhere else it was ping-pong, and we don't know how to play ping-pong," he said.
"Our game is on the ground, and the ball wouldn't move. We did what we could - the ref made a decision, a human being can make a mistake."
Libya's Brazilian coach Marcos Paqueta said: "It was hard for both teams to play in these conditions. "I think the result was deserved. We were up against a very good Zambia side, the group favourites. We still have a chance to qualify."
Thursday's Group B programme sees Sudan up against Angola and Côte d'Ivoire taking on Burkina Faso.