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."
Menezes took over in July 2010 and dispensed with the old guard in favor of youngsters like Neymar, Lucas, Thiago Silva and Oscar.
Although his team have won 22 of their 33 matches, they have failed to overcome top-class sides like Germany, Argentina and the Netherlands.
The former Corinthians coach is under pressure to produce an exciting and winning side ahead of the 2013 Confederations Cup and 2014 World Cup, both of which will be held in Brazil.
His players struggled to impose itself against a team 62 places below then in the world rankings and it was not until he introduced Hulk and several others that Brazil began to create real chances.
"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.
