Samson Siasia, Nigeria's caretaker coach for the qualifiers after Sunday Oliseh's shock resignation started the match with Odion Ighalo , Ahmed Musa and Kelechi Iheanacho staring in a three- pronged attack for the host team.
Obaobona started in the heart of the defence for the super Eagles while new captain John Mikel Obi started alongside Etebo in the heart of midfield as Siasia wanted his team to come out with all three points at home ahead of a tricky away tie in Egypt.
Nigeria pressurized in the first half with efforts from Etebo, Odion Ighalo and Kelechi Iheanacho unable to break the Egyptian defence down as the match ended 0-0 in the first half.
The second half began with Oghenekaro Etebo scoring in the 59th minute after an Iheanacho shot caused a rebound to which Etebo gladly put into the net.
Alex Iwobi was introduced with 8 minutes to go as he made his first competitive debut for Nigeria and tried with his teammates to increase Nigeria's lead over Egypt
Nigeria had chances to increase their lead with efforts from Etebo, Victor Moses and Ighalo unable to increase the lead.
With three minutes of extra time added, Mohammed Salah , Egypt's star man scoring after the Nigerian defence played him onside, much to the delight of the away team.
The pain and sadness on Samson Siasia's face was too evident to see as 20,000 Nigerian fans at the stadium in Kaduna left unhappy after seeing the home team drop two valuable points.
At the moment, Egypt are on top of group G with seven points from two matches, while Nigeria are two points behind with only the overall group winners guaranteed automatic passage to AFCON 2017 in Gabon.