Walker made two alterations to last week’s starting lineup with David Abagna Sandan and Dominic Nsobila taking the places of Jonah Attuquaye and Evans Osei-Wusu respectively.
The Super Eagles dominated the first half of the match but failed to create scoring opportunities as Ghana’s defence reacted very well to keep the game barren.
Nigeria continued with their dominance in the second half and finally got the breakthrough in the 76th minute through Zulkilfilu Muhammed.
Ghana goalkeeper Danlad Ibrahim made a fantastic save to deny Nigeria a second goal moments later.
The Super Eagles got the second goal to level matters on aggregate after Nigeria League top scorer Chijioke Nnamdi Akuneto netted in stoppage time to force the tie into penalty shootouts.
The Black Galaxies secured their first qualification to the CHAN tournament for the first time since 2014 as they won 5-4 in the penalties.
Ghana scored all five of their kicks with Great Olympics’ Amos Acheampong netting the winning goal while Nigeria missed one.