The Denmark-based striker scored in the opening five seconds of the first half, when he fired a thunderous shot past Egyptian goalkeeper, Abdelrehim Mahmoud from outside the 18 yard box.
It was one of fastest goals that will go into football history.
According to Total Sportek, Damian Mori, an A-League striker scored a goal in 3.69 seconds for his Adelaide City club against Sydney United in 1995.
Ex-Arsenal and Germany International, Lukas Podolski has a record of scoring another fast goal, when he scored in 6 seconds in an international friendly between Germany and Ecuador in 2013. FIFA recognises this as the fastest goal in international football.
Onuachu will now take over the mantle from Podolski.
The early goal however spurred the Egyptians as they took control of the midfield, putting the Nigerian defence line, led by William Trost-Ekong under pressure.
Ekong, who arguably was one of the outstanding performers in the Nigerian team, however sustained a head injury, and had his head bandaged.
Upon the resumption of the second half, Nigerian coach, replaced goalkeeper Daniel Akpeyi with Ikechukwu Ezenwa.
The Egyptians mounted sustained attacks on the Nigerian defence, but were kept at bay by the duo of Ekong and Leon Balogun.
Nigerian coach, Gernot Rohr made two changes, as John Ogu made way for Semiu Ajayi, while Etebo Oghenekaro came in place of Alex Iwobi.
In the 88th minute of play, Rohr pulled out goalscorer, Onuachu, who looked tired, and brought in Odion Ighalo.
Nigerian goalkeeper, Ikechukwu Ezenwa made two brilliant saves in the added time of the game to deny the Egyptian dangerman, Abdelmegid Islam.
In a post-match media conference, Egyptian coach, Javier Aguirre applauded the performance of his team even in defeat.
“We played good football today, and I must commend my players though we lost to Nigeria.
“We will take the positives from this friendly back home, as we continue to prepare our team for the AFCON.
He said the absence of Mohammed Salah, Africa’s footballer of the year, was not felt by the team, as there were other great young players.
On his part, Nigerian coach, Gernot Rohr said the game was a great match for both teams, as they continue their preparations for the AFCON.
“To me, today’s game is not just a good match, but a great one for both teams. Both teams played good football,” Rohr said.