"I am very happy today, but not really about the result," Keshi said.
"I am happy about the way the team played, the way they passed the ball, the build-up, all the things we talked about in training, they did in the second half."
The first half was less pleasing for the coach.
"They were a bit too anxious to score in the first half, but at half time, I told them to calm down and just be patient and the goals would come.
"And when we came back, the second half was much better."
With the 2-0 win, the Super Eagles finished second in the group, after Burkina Faso drew 0-0 against Zambia.
Nigeria will stay in Rustenburg, where they will play Group D winners Cote d'Ivoire on Sunday.