Orioles right-hander Mike Wright brushed Bautista with an 0-1 pitch, prompting warnings from home plate umpire C.B. Bucknor. Gibbons came out and was ejected for the second time before engaging in a lengthy discussion with crew chief Dale Scott.
Gibbons said he was "a little bit shocked" at the spate of ejections.
"There was a little paranoia or something there," he said.
Bautista has a history with Orioles reliever Darren O'Day dating to 2013. Earlier this season, Bautista argued with Baltimore's Adam Jones during an April 21 game in Toronto after Orioles rookie Jason Garcia threw behind the Blue Jays slugger.
Bautista, who traded words with Baltimore's dugout after being hit, didn't bite when asked how he felt about the incident.
"I'm not going to contribute to turn this into TMZ or a gossip column," he said.
Jones wasn't too bothered about being hit, but did say the warnings might have been premature.
"I wasn't too happy when the warnings came out immediately," Jones said. "The umpires are trying to get a hold of the game. I understand it."
Orioles manager Buck Showalter came out between innings to argue with Bucknor but was not ejected.
The back-and-forth came in the midst of Jays starter Marco Estrada taking a no-hitter into the eighth inning. Batting for Steve Pearce, pinch hitter Jimmy Paredes broke it up with a bloop single to left to begin the eighth, ending a streak of 15 straight outs. Bench coach DeMarlo Hale, filling in for Gibbons, immediately came out and replaced Estrada, who threw a season-high 118 pitches, with Roberto Osuna.
"I wanted to keep going," Estrada said. "If I had to throw 200 pitches today, I would have."
Dave Stieb still has thrown the only no-hitter in Blue Jays history, doing it against Cleveland on Sept. 2, 1990.
Tensions did not end there. With two on and the Blue Jays leading 5-1 in the eighth, Osuna and Hale were ejected after hitting Jones on a 3-1 pitch. An inning later, Brett Cecil hit O's right fielder Chris Parmelee on the wrist but was not thrown out. That brought Jones to the plate, and he hit a two-run single to right that cut the lead to 5-4. Jones, who returned after missing three games with a sore right shoulder, was 1-for-3 with a walk.
Chris Davis struck out to end the game.
The Associated Press contributed to this report.