The spot-kick was awarded ten minutes into extra time when Diego's goal-bound shot was intentionally handled by defender Cory Gibbs who was red carded for the offence.
"The ball was going in the goal," Gibbs said.
"The only chance I had to do something to prevent the loss was that. That's the way it goes and the ref saw it."
The winning goal capped a stirring fightback for the Brazilians who dominated most of the match, but fell behind in the 62nd minute when Carlos Bocanegra headed in a Claudio Reyna free kick to give the U.S. a surprise 1-0 lead.
A pro-Brazilian crowd of 35,211 welcomed the goal in a match that appeared to be headed towards a goalless stalemate.
Brazil, fielding its under-23 side, intensified its efforts to break down the U.S. defence and nearly pulled level in the 74th minute when Julio Baptista was foiled by an acrobatic Kasey Keller save.
However, the Brazilians were finally rewarded a minute from time when Kaka latched onto a rebound to beat Keller from eight metres.
"It was a very exciting game," Brazil coach Ricardo Gomes said.
"We dominated much of it, but had a lot of difficulty getting through. The U.S. never gave up on offence, they put a lot of long balls into the area and they ended up getting a goal that way.
"Overall, I think the amount of plays we made and the opportunities we had, we couldn't leave here without a win.
"When we suffered that goal, our quality as a team was that we remained composed and came back to win the game."
DEFENDED WELL
Brazil now await the winner of Thursday's other semi-final between Mexico and Costa Rica at the Azteca Stadium in Mexico City, the site of Sunday's final.
"We ran out of gas out there," Keller said. "It was really tough giving up the goal right at the end of the game because we had defended so well.
"As extra time came, we were drained and I knew that we were going to have to hang on for dear life."
The U.S. face the loser in the third place game in Miami on Saturday.
The match was the second meeting between the two teams in the past six weeks following a 1-0 victory for Brazil's senior side in the opening round of the Confederations Cup last month in France.
Historically, the U.S. has lost 11 of 12 fixtures against Brazil with the only victory coming in the semi-finals of this tournament in 1998.
