The slugger started walking toward the mound, and Greinke appeared to say something. Quentin then charged the 2009 AL Cy Young Award winner. They dropped their shoulders and collided, and Quentin tackled the pitcher to the grass.
Quentin and Greinke ended up at the bottom of a huge scrum as players from both sides ran onto the field and jumped in.
Dodgers slugger Matt Kemp, ejected following the fight, confronted Quentin as they were leaving Petco Park after the game. The two went nose-to-nose briefly before Padres pitcher Clayton Richard stepped between them. Police and security broke it up.
Both teams said the melee could have been avoided.
"I never hit him on purpose," said Greinke, who had his left arm in a sling and appeared shaken after the game. "I never thought about hitting him on purpose. He always seems to think that I'm hitting him on purpose, but that's not the case. That's all I can really say about it."
Asked whether there was bad blood between the teams, Greinke, who twice hit Quentin with pitches when they were in the American League, said: "Now there probably is. I don't know if there was beforehand."
He said the injury was "awful. It's silly that something could happen like that. I'm disappointed."
Dodgers manager Don Mattingly was livid, saying it shouldn't have happened because Quentin was hit on a 3-2 pitch in a one-run game.
"That's just stupid is what it is," Mattingly said. "He should not play a game until Greinke can pitch. If he plays before Greinke pitches, something's wrong. He caused the whole thing. Nothing happens if he goes to first base."
Quentin said his history with Greinke has been "well documented. That situation could have been avoided. You'd have to ask Zack about that."
"I've been hit by many pitches," said Quentin, plunked more often than any other major league hitter since the start of 2008. "Some have been intentional, some have not been. For the amount I have been hit and my hitting style, I'm going to repeat: I have never reacted that way."
Quentin and Greinke have a history.
The right-hander now has hit Quentin three times with a pitch, with the last before Thursday coming in 2009. Quentin is the only batter Greinke has hit three times, according to ESPN Stats & Information.
Quentin led the majors in hit by pitches in both 2011 (23) and 2012 (17). He's been hit 116 times in his career (seventh-most among active players), and he left Tuesday night's game against the Dodgers after being hit on the right wrist with a pitch.
When Quentin and Greinke were finally pulled apart, Quentin was led off the field by teammate Mark Kotsay. Greinke was checked by a trainer and Mattingly before walking off toward the dugout, his uniform top disheveled after it had been pulled over his head by Quentin.
Greinke lowered his left (non-throwing) shoulder into Quentin and took the brunt of the blow as they collided. The right-hander, who had his wife and in-laws in the stands, joined the Dodgers as a free agent in the offseason, signing a $147 million, six-year contract.
He missed time during spring training with a tender right elbow and the flu. Quentin was slowed by a balky right knee after having offseason surgery.
After the teams started going back to the dugouts and bullpens, Jerry Hairston Jr. came running across the field yelling and pointing at someone in the San Diego dugout and had to be restrained.
Kemp also was livid, perhaps in part because Padres starter Jason Marquis threw a high-and-tight pitch to him in the first inning.
Kemp was angry after finding out the severity of Greinke's injury.
"I'm asking Greinke if he's OK, and he said his shoulder's messed up. That kind of took me over the edge right there," Kemp said.
"I think Carlos Quentin went to Stanford, something like that?" Kemp said. "I heard there's smart people at Stanford. That wasn't too smart. Greinke didn't do anything wrong. That stuff happens in the minor leagues. It doesn't happen in the big leagues."
The benches and bullpens emptied again, leading to pushing and shoving. But it did not appear any punches were thrown.
Quentin, Kemp, Hairston and Greinke were ejected. Los Angeles reliever Chris Capuano was given all the time he needed to warm up when play finally resumed after a delay of about 15 minutes.
Following the game, the Dodgers announced that Greinke has a broken collarbone.
Quentin was hit by a pitch above the right wrist by Dodgers reliever Ronald Belisario on Tuesday and had to leave the game. He sat out Wednesday night's game.
Greinke plunked Quentin once in 2008 and once in 2009, according to STATS. Coming into the game, Quentin was 6-for-24 with three homers against Greinke.
Greinke has hit 46 batters since his big league debut in 2004.
Uribe homered to left on a 3-2 pitch from Luke Gregerson (1-1) with one out in the eighth to give the Dodgers a 3-2 lead.
Former San Diego star Adrian Gonzalez hit a two-run homer deep into the seats down the right-field line with two outs in the first off Marquis, his first. Carl Crawford was aboard on a leadoff single.
Marquis allowed two runs and seven hits in five innings, struck out five and walked four.
The Dodgers took two of three from the Padres. ... L.A. heads to Arizona for a three-game series starting Friday night, with LHP Clayton Kershaw (2-0, 0.00 ERA) scheduled to face LHP Patrick Corbin (1-0, 3.00). The Padres open a three-game home series against Colorado, with RHP Tyson Ross (0-1, 4.50) scheduled to face RHP Jon Garland (1-0, 3.00). ... Andre Ethier singled in the seventh to extend his hitting streak to 11 games. ... Greinke reached 1,500 career innings. ... The Padres dropped to 2-7, matching last year's start.
Information from The Associated Press was used in this report.