The Blue Jays suspended Pillar on Thursday shortly after he apologized, saying he was "completely and utterly embarrassed" by his actions toward Jason Motte.
Freeman was hit by Toronto's Aaron Loup during the fifth inning of an 8-4 victory over the Blue Jays on Wednesday night.
Replays appeared to show Pillar using the slur as he shouted toward the mound.
The 28-year-old still could face disciplinary action, though, as Major League Baseball confirmed Thursday it is investigating Pillar's remarks.
"The Toronto Blue Jays are extremely disappointed by the comments made by Kevin Pillar following his at-bat during the 7th inning of last night's game", it said.
It's not the first time the Jays have suspended a player over the use of a homophobic slur.
Pillar told reporters in Atlanta there is "no place for this language" anywhere, including on the baseball field.
On Thursday, MLB Commissioner Rob Manfred was asked about the incident at the conclusion of the league's quarterly owners meetings in NY. The Braves went on to win 8-4.
It's the second home run by a pitcher in Blue Jays history, with Mark Hendrickson (2003) the other.
"That's something making the game tough to watch", he said, per ESPN.com.
The investigation is likely more a discussion about what to do in terms of a possible fine and/or suspension along with attachments such as sensitivity counseling, because it was pretty clear what Pillar said and he seemed to be admitting wrongdoing after the game.
Dwight Smith Jr., the son of the former outfielder who played for four teams, including the Braves, was recalled from Triple-A Buffalo to replace Pillar on the roster.
"It's turning to look at me stuff, it's not even about winning anymore".
That doesn't excuse him for the comment, but it's encouraging to see that he knows the mistake he made and feels bad about it. I'm just exhausted of it.
After the game, O'Flaherty delivered a withering line about Bautista: "I'm surprised he's ready to fight again after previous year".
Benches emptied in Wednesday night's game in Atlanta after Bautista homered to left field, stood at home plate and stared toward pitcher Eric O'Flaherty before flipping the bat away with an authoritative toss.