The Eagles beat the Elephants of Cote d’ Ivoire 2-1, to clinch a semi-final ticket at the tournament.
A message on the Twitter account of the Special Adviser to the President on Media and Publicity, Dr Reuben Abati, said Jonathan thanked the players “for their masterly and superlative performance.
“President Jonathan thanks the Super Eagles for their masterly and superlative performance in the just-concluded AFCON encounter with CIV.
“President Jonathan says to the Super Eagles now is the time to really begin to soar like the Super Eagles that they are.
“President Jonathan joins all Nigerians in celebrating today’s victory by the Super Eagles of Nigeria.
“The President has watched all the matches, including this last one.”