Mexico face Jamaica away next Tuesday in a CONCACAF World Cup qualifier and Nigeria face Kenya in an African qualifier on Wednesday.
CONCACAF Gold Cup holders Mexico and African champions Nigeria are taking part in the Confederations Cup in Brazil from June 15 to 30.
Hernandez put Mexico ahead in the 21st minute of Friday's match from Pablo Barrera's right cross but six minutes later Barrera was sent off for preventing a Nigeria goal with his hands.
Brown Ideye equalised for Nigeria from the penalty spot and John Ugochukwu put them ahead with a shot in the 39th minute that took a deflection off Gerardo Torrado.
Manchester United striker Hernandez's equaliser came from Carlos Salcido's left cross 20 minutes from time.
Mexico are in the precarious place of fifth in the six-nation final CONCACF group with three points from three draws.
The top three at the end of the series in October will go through to next year's finals in Brazil and the fourth-placed team will play off against Oceania winners New Zealand for another berth.