Menezes sent out an attacking team but they struggled to break down the dogged South Africans and the match was only decided in the 74th minute with a goal from second-half substitute Hulk.
The striker signed by Zenit St Petersburg last week for 55 million euros had been on the pitch for less than 10 minutes when he pounced on a rebound to turn and smash the ball home from 12 yards.
Menezes acknowledged the team did not gel but said fans' boos that began in the middle of the first half were not helpful.
"[The boos] are uncomfortable," he told reporters. "The younger a team is the more it feels the lack of support."
"We lost a little bit of control of the game for 15 minutes in the second half, but with the substitutions we took control again and that was enough to give us a result," Menezes said.
"I don't think we played really badly. Maybe we didn't play well but we weren't really bad."
Brazil's next match is against China in Recife on Monday.
