Rohr had cut his initial 30-man provisional squad to 26 while injury ruled Moses Simon out of the 2018 FIFA World Cup.
After the game against England on Saturday, June 2, Super Eagles boss further cut the squad to the final 23-man ahead of the 2018 World Cup, leaving out Aina and Agu.
Aina and Agu will be on standby in case of any other injuries to any of the players in the 23-man squad and will not make the journey to Austria where the Super Eagles will be camping ahead of the 2018 World Cup.
Aina has made just five Super Eagles appearances since his debut in October 2017. In his last appearance for the Super Eagles, the Chelsea defender who spent last season on loan at Hull City conceded a penalty in Nigeria's 1-1 friendly draw against DR Congo.
In his place, Rohr has chosen to go with the experience of Elderson Echiejile.
Although a regular call-up under Rohr, Agu made just three appearances for the Super Eagles during the 2018 World Cup qualifiers.
In his place, Rohr opted for Torino midfielder Joel Obi who has featured heavily in the warm-up games ahead of the 2018 World Cup.
Obi didn’t play a single game during the qualifiers and only got a recall to the Super Eagles in March.
Crotonestriker Simeon Nwankwo is another latecomer to the side, getting his first Super Eagles call-up in the 30-man provisional squad for the 2018 World Cup.
Simy made his Super Eagles debut in the 1-1 draw against DR Congo.
Captain Mikel John Obi is one of the five players in the 23-man squad that have played in the FIFA World Cup.
Mikel, Victor Moses, Ogenyi Onazi, Ahmed Musa and Kenneth Omeruo were all part of the Super Eagles squad under late Stephen Keshi to reached the round of 16 of the 2014 FIFA World Cup in Brazil.
The 23 players have headed to Austria where they will camp at the Avita Resort in Bad Tatzmannsdorf before moving to Russia for the World Cup proper.
Super Eagles 23-man squad for 2018 FIFA World Cup
Ikechukwu Ezenwa (Enyimba), Daniel Akpeyi (Chippa United) Francis Uzoho (Deportivo)
William Troost-Ekong (Bursaspor), Leon Balogun (Brighton), Kenneth Omeruo (Chelsea on loan to Kasımpaşa), Brian Idowu (Amkar Perm), Chidozie Awaziem (Nantes) Shehu Abdullahi (Bursaspor), Elderson Echiéjilé (Cercle Brugge), Tyronne Ebuehi (ADO Den Haag),
John Obi Mikel (captain) (Tianjin TEDA), Ogenyi Onazi (Trabzonspor), John Ogu (Hapoel Be'er Sheva), Wilfred Ndidi (Leicester City), Oghenekaro Etebo (Las Palmas), Joel Obi (Torino)
Victor Moses (Chelsea), Alex Iwobi (Arsenal), Odion Ighalo (Changchun Yatai), Ahmed Musa, (Leicester City), Kelechi Iheanacho (Leicester City), Simeon Nwankwo (Crotone).