Victor Moses set the African giants on their wa
y from the spot after a controversial penalty was awarded by match official Bakary Gassama for an unintentional hand-ball from Aynalem Hailu.
Saladin Said then had a notable penalty appeal turned down in the second half, although Bishaw feels the tide had already been turned by the award of Moses' spot-kick.
"I respect [Nigeria boss Stephen] Keshi; he has done a good job organising this team," the 61-year-old told reporters.
"But the ref cheated us. We had two penalties denied us. And then he awarded one wrong one to Nigeria.
"That penalty to Nigeria affected the tide.”
A free kick from Victor Obinna settled matters in Calabar and ensured the Africa Cup of Nations champions will enter the draw for the World Cup group stage on December 6 with a 4-1 aggregate win.