The Super Eagles went into the clash at Free State Stadium needing victory to keep their hopes alive, but were forced to settle for a 1-1 draw after a tense encounter.
With Nigeria still six points adrift of South Africa in Group C and only two games remaining, Chelle acknowledged their hosts matched them on the night.
"We tried, [the players] gave everything to try to win and, like I said, it's difficult to come here and hope for a win because this team is very good, their wingers are very fast, and the striker keeps the ball well," said Chelle.
"During this game, for just 10 seconds, we were not in a good position and they killed us, so after that we came back in the game because we were ready for that, and the state of mind of the players was to come back and try to score a goal, but South Africa is a good team."
Nigeria must still face Lesotho and Benin, with the hope that Bafana drop points against Zimbabwe and Rwanda, and Chelle conceded their fate has not been in their own hands all along.
"We are professional, so it's still two games and for sure these players want to win these two games, but at this moment is difficult for us because we wanted to win [against Bafana], and I think we did everything [to try and win]," he added.
"So in the two last games, a lot of things can happen in one month, and for sure a lot of things about the points, about the team, about everything, so we just need to analyse this game again and after that we'll see in the last two games."