The 25-19, 25-17, 25-20 quarterfinal victory was costly for the top-ranked Brazilians, who lost opposite spiker Leandro Vissotto Neves to what appeared to be a groin injury.
Brazil goes on to face the winner of the afternoon match between the United States and Italy in the semifinals on Friday.
Cristian Poglajen couldn't control Endres' spike for match point. Facundo Conte led No. 8 Argentina with 10 points.
Argentina went into the match with a 2-3 edge over Brazil in Olympic play. Argentina defeated Brazil 3-2 for the bronze medal in the 1988 Seoul Games, the team's best Olympics finish in the sport.
The Brazilians have won the gold medal twice, most recently in the 2004 Athens Games. The United States and Russia are atop the medals table with three golds each since volleyball became an Olympic Sport in 1964.
Brazil claimed the silver medal in Beijing, falling in a 3-1 upset by the undefeated U.S. men. Argentina hasn't played in an Olympics since Athens, where they finished fifth.
Brazil went up 19-11 in the first sent on Dante Amaral's kill. But moments later Vissotto Neves crumbled to the court.
Neves was the second-leading scorer on his team during the Olympic competition with 48 total points before he was injured. He limped off the court at the end of the match. The extent of his injury was unclear.
Brazil claimed the first set on Endres' spike.
Endres, the younger brother of Brazilian volleyball great Gustavo Endres, spiked to put Brazil in front 21-16 in the second set, and Sidnei dos Santos Junior finished it off with an ace for a 2-0 advantage.
The young Argentines were able to keep up better than the Brazilians in the final set, but never managed to pull ahead.
Brazil coach Bernardo Rezende didn't play captain Gilberto Godhoy Filho, who is known as Giba, preferring to go with his younger players. One of the game's most celebrated stars, Giba hasn't started a match in London.
The Brazilian fans in the crowd at Earls Court were not happy about Giba's absence and many started chanting his name in the third set.
Giba, named MVP of the competition at the Athens Games, had surgery to help his left leg heal a tibia fracture earlier this year.
Brazil won the 2010 World Championship before claiming the silver in the 2011 World League and the bronze in the 2011 World Cup, which qualified the team for the Olympics.
But there were questions about Brazil's health when the team missed out on the semifinals of this year's World League for the first time since 1988.
Argentina coach Javier Weber retooled his team in 2010, going with his younger players in the run-up to the Olympic Games.
Brazil's only loss in the preliminary round came to the U.S. men, who finished atop their pool, while Argentina was the only team in its pool to defeat Bulgaria.