His replacement, T.J. McFarland, then gave up the game-winning single to Martin Prado in the 13th, and the Orioles lost to the Miami Marlins 1-0 Saturday.
Orioles manager Buck Showalter shrugged off the impact of the ejection, saying Matusz would have faced only one more hitter anyway.
"He wouldn't have pitched the next inning," Showalter said.
Matusz might not pitch again for a while. The Brewers' Will Smith was suspended for eight games Friday by Major League Baseball for having a foreign substance on his arm in a loss to the Braves.
Matusz entered the game in the 12th with the score 0-0 and retired the first two batters before new Marlins manager Dan Jennings approached home plate umpire Jordan Baker. Baker and crew chief Paul Emmel then went to the mound to inspect Matusz's arm.
"I went out there and told the pitcher I was going to touch his right forearm," Emmel said. "That's where he was touching before he went to the ball. I detected a foreign substance, so the pitcher was ejected."
Showalter joined the conversation with no argument.
Matusz declined to say much about it.
"We're not going to address the issue right now," he said. "Obviously I have my own personal opinions about the issue, but right now with emotions running high we're going to let this settle and address questions at a later time."
Jennings said the Marlins noticed Matusz using a suspicious substance.
"We saw something shiny on his arm," Jennings said. "We watched a couple of pitches to make sure he went to it. By their opinion there was a foreign substance there, they made their decision."
The Marlins broke an eight-game losing streak and improved to 1-8 on their homestand. Jennings earned his first career victory in six games as a manager, then received a dunking from his players in the nightclub swimming pool adjacent to the clubhouse.
Jennings was unable to pinpoint who dunked him in the pool.
"No, the shaving cream pretty well blocked my vision," he said with a laugh. "It's the best, dirtiest bath I've ever had."
Five Miami relievers combined to pitch the final seven innings while allowing only two baserunners. Carter Capps (1-0) struck out six in the final three innings.
Adeiny Hechavarria walked to start the 13th against McFarland (0-1). Hechavarria took third on a two-out single by Marcell Ozuna. Giancarlo Stanton was then intentionally walked to load the bases.
Prado lined a 1-1 pitch into right-centre field.
"It kills me because I know everybody out there did everything they could to win," McFarland said. "That's the worst part for me. It hurts that I wasn't able to come through for the team."
Baltimore's Mike Wright allowed three hits in seven scoreless innings and has yet to give up a run through 14 innings in two career starts. The last of his 98 pitches was a 96 mph fastball to strike out Michael Morse with runners at the corners to end the seventh.
Wright's scoreless streak to begin his career is the longest by an Orioles pitcher since Dave Ford started with 15 consecutive shutout innings in 1978, according to STATS.
Oliver Drake, recalled before the game from Triple-A Norfolk, pitched three scoreless innings in his major league debut.
The Orioles went 1 for 10 with runners in scoring position. Miami centre fielder Ozuna kept the game scoreless in the sixth when he threw out Travis Snider trying to score from second on Wright's two-out single, the first career hit for the pitcher.
Mike Weaver, son of Orioles Hall of Fame manager Earl Weaver, threw out the first pitch. He was accompanied by Earl's widow, Marianna.
Orioles RHP Tyler Wilson, who earned his first major league victory pitching in relief Friday, was optioned before the game to Norfolk.
Orioles RHP Bud Norris (bronchitis) will make his second rehab start Wednesday for Double-A Bowie.
RHP Miguel Gonzalez (5-2, 3.24) is scheduled to start the series finale Sunday for the Orioles against RHP Tom Koehler (2-3, 3.70).