Hearts of Oak captain Thomas Abbey missed the game due to injury while Isaac Twum lasted only four minutes.
Two second half goals from Anthony Okpotu and Peter Moses handed the Super Eagles the win and a ticket to join the last four.
“It is not about the goals we conceded. It is rather about how fit our players were before and during the game," Konadu said.
“There was no time to recover properly for this important match but all the same, the boys managed. Some were carrying injuries but we managed to go through the match.
"Most of the players got injured in the first half but we did not have the opportunity to replace them. Isaac Twum, for instance, got injured in the warm up and he thought he could play with it. Unfortunately, we had to replace him.
"However, Nigeria were the better side in the game and we all agree with that,” he added.
Ghana will lock horns with runners-up of Group B at the Cape Coast Sports Stadium while Nigeria take on the winners for a place in the final.