Perez was visibly upset, and manager Manny Acta and pitching coach Randy St. Claire had to restrain him as he continued to argue with Hernandez.
After the game, Perez didn't hide his anger at the calls or Hernandez, who Perez said has called four balks against him in his career.
"That's the third or fourth time he called [a] balk on me," Perez said of Hernandez after the game. "I lost the game twice. It's like he's got something personal against me. And I hate that.
"I'm a professional. I want to be there as long as I can because I don't want to see my teammates in the bullpen go out there and throw so many pitches or throw so many innings. I hate that."
While Acta said he understood why his player reacted the way he did, he felt Perez's ejection put his team in a tough situation with just 2 2/3 innings in the books.
"Of course, I understand his reaction, but where did his emotions get us?" Acta said after the game. "They didn't erase the balks, they didn't put a run for us on the board, and meanwhile, we killed our bullpen. ... That really didn't help us."
Perez's catcher, Jesus Flores, said he didn't think the pitcher's move was a balk, but rather a legitimate pickoff attempt. He sympathized with the ejected pitcher after the game.
"I didn't see anything wrong," Flores said of the pickoff throw that resulted in the second balk. "I understand why he was upset."
Hernandez declined comment through a spokesperson after the game.
Perez said he isn't worried about getting fined or suspended by Major League Baseball. He said he wanted to "protect" his teammates and specifically his bullpen, which worked 6 1/3 innings in relief after his ejection.
"I know I'm going to get fined, but I don't care," a heated Perez said in the clubhouse after the game. "I've been doing the same ... move the entire year. So why does he have to call it twice in the same inning? For them to score a run against me then I lost the game, he might be happy now."
After the game, Acta characterized the balk calls as "a little mind boggling."
"This guy takes the mound for us every five days and nobody else calls a balk on him, and this guy drops two on him in one night," Acta said.
Acta confirmed Hernandez said Perez was stepping toward the plate on his pickoff moves.
"I went towards home plate and then I threw over," Perez said, describing what Hernandez said he did. "I've been doing the same thing [all year], and he called it. I don't know what it is [he has] against me, and I don't like that. I hate that. I lost the game, I hate that so bad."
Perez has 16 balks in his 11-year career, but the pair Tuesday night were his first two of the year and first called against him since 2006.