Amapakabo, 49, who is the team’s first assistant, is to take charge of the squad against Libya in next month’s second round of qualifying for the 2019 African Under-23 Cup of Nations finals.
It is unclear whether Yusuf will return to his post at the end of his ban in September.
Amapakabo was second assistant to Nigeria’s senior team’s coach Gernot Rohr at the recent World Cup in Russia and worked with Yusuf as Nigeria finished runners-up at last year’s African Nations Championship (CHAN) in Morocco.
His immediate task will be to secure a third successive qualifying spot and retain their continental title at the U-23 Cup of Nations scheduled for Egypt in November.
The event serves as a qualifying tournament for the 2020 Olympics, where the top three teams will book their place in Tokyo.
Nigeria – bronze medallists at Rio 2016 – won the 1996 Olympic football tournament and are the first African country to complete an Olympic medal sweep having won a sliver medal in Beijing in 2008.