After the second strike, Beltran started talking to Runge, who took off his mask and continued the dialogue before he brushed dirt off home plate. Manuel then came out and started arguing.
"I thought that Mr. Runge was kind of baiting Carlos," Manuel said. "That's how I saw it, I could be wrong. So I wanted to go out and make sure everything was OK, and it got a little heated."
Runge appeared to bump into Manuel before throwing him out of the game. The manager walked to the bench after getting a few more words in as the Shea Stadium crowd roared.
Beltran continued the conversation and Runge quickly threw him out the game. An incensed Beltran then got in Runge's face and had to be held back before Manuel came out to escort his center fielder to the dugout.
"He really bumped Jerry to get him an excuse to throw him out of the game," Beltran said, "and I just let him know that that was weak, the move that he did, you know just being able to do that and he throws me out of the game.
"This is the first time that I've been so angry in my career."
Beltran said Runge should be punished, too, if Major League Baseball decides to fine or suspend him.
"That was horrible," Beltran said.
Runge declined comment after the game.
Manuel was promoted from bench coach to manager after the Mets fired Willie Randolph last week. New York lost 5-2 to Seattle on Monday night in Manuel's first game at Shea Stadium since the switch.