Super Eagles coach Gernot Rohr made a couple of changes to his team as Daniel Akpeyi was between the post while Leon Balogun returned to partner Williams Troost-Ekong in central defence.
John Ogu got a start alongside Wilfred Ndidi in midfield while Onuachu got his first start for the Super Eagles.
In just his second game for the Super Eagles, Onuachu received a pass from Ogu and after his first touch, he let out a low drive from just outside the area which beat Egyptian goalkeeper Mohmoud Genesh with the first touches of the game.
The Stephen Keshi Stadium in Asaba erupted with the early goal as the shell-shocked Egyptians tried to put themselves together.
The Super Eagles from there were very comfortable although the Pharaohs were putting together a couple of passes.
The Super Eagles were enjoying possession and around the 10th to 12th minute, they threatened twice from a corner which Ndidi headed wide the first but failed to connect with the second from good area.
The Egyptians were get themselves together and were putting together a couple of passes but did not really trouble the Nigerian defence.
The Super Eagles were still dangerous anytime they went forward and Moses Simon did well to beat his man but his follow up pass to Onuachu in the 23rd minute was poor.
Three minutes later, Ndidi, Alex Iwobi and Simon combined well just outside the area but the final ball did not connect.
The Egyptians got their first chance of the game in the 29th minute but a header from a cross went well over the bar.
A minute later, the Super Eagles got another chance as a loose ball fell to Iwobi after an Egyptian defender failed to clear but the Arsenal man could not connect with the ball properly.
It was 1-0 to Nigeria at the break and the Super Eagles continued from where they stopped in the second half.
With Ikechukwu Ezenwa in goal, the Super Eagles continued to keep the ball well with some fantastic passing especially in midfield as Ogu and Ndidi dictated play.
Ogu was soon replaced by Semi Ajayi after he picked up an injury.
The Egyptians troubled the Super Eagles defence twice in the 69th minute but two dangerous cross from the right were cleared by Troost-Ekong.
Henry Onyekuru did some good work midway in the second half, first getting past two men at the edge of the area before beating his man for pace in the 77th minute but his final balls in those two occasions did not meet a teammate.
The Egyptians had a penalty appeal turned down after an Egyptian player fell in the Nigerian box after a challenge from Jamilu Collins but the referee was not having it.
The Egyptians almost got an equaliser in the 85th minute after Balogun was caught out of position but the Brighton & Hove defender recovered quickly to make a last-ditch tackle.
In the 89th minute, Ezenwa made two good saves to stop the Egyptians, diving well to save a shot from outside the box and then getting down quickly to save again after an Egyptian had gotten onthw rebound.