The Black Satellites took the lead mid-way through the first half and tried to dominate the game but the Flying Eagles resisted.
The Nigeria team, made up of the majority of the players who won silver at the Fifa Under-17 World Cup finals on home soil last year, snatched the equalizer in the last ten minutes through Omoh Ojabu.
Ghana will play Brazil next on April 10 in a repeat of the Fifa Under-20 World Cup.
The tournament is being organised by the South Africa Football Association to test facilities for the Fifa World Cup finals.
The tournament is envisaged to become an annual event and become a legacy of the Fifa World Cup 2010 events.
Hosts South Africa beat Brazil 3-2 in the late game at Newlands Stadium.
South Africa will play Nigeria and Ghana will face Brazil at the new Cape Town International Stadium on Saturday afternoon.