Lillard confirmed to ESPN that the phrases were shouted at him after the Blazers' 108-107 loss to the Timberwolves in Minnesota.
"I don't bother nobody," Lillard told ESPN. "They were straight disrespectful."
Cellphone video captured an irritated Lillard approaching the hecklers, asking, "Which one of you all said that?" A woman in the area pointed out one of the individuals, and that person apologized. Sources at the scene say no action was taken against the fans.
Athlete Ally, a non-profit group trying to end homophobia in sports, issued a statement on Tuesday.
"The use of these homophobic slurs have no place in sports or in society," Executive Director Hudson Taylor said. "Fan sections remain one of the most unsafe places for the LGBTQ community, and will remain so if these slurs aren't met with condemnation and continued education."
When Lillard was confronted, he likely wasn't in the best mood.
The two-time All-Star played 37 minutes, finishing with 17 points and 13 assists, and was miffed that Portland attempted only five free throws during the game. Minnesota went to the line 21 times.
Lillard, one of the best drivers and finishers in the league, had one free throw attempt. He let his frustration be known immediately after the game.
"We had a lead," Lillard said of Portland's 10-point advantage midway through the fourth quarter. "I think, on our part, that was the main thing is the  turnovers. ... Maybe those get cut in half if you're not allowed to grab and all that stuff. Half of those things may not happen.
"Maybe we've just got to be stronger with the ball and make smarter plays. ... At crucial moments, we're making plays and trying to score and guys [are] getting hit, guys literally out there grabbing my arms. I got hit in the face one time, and it's like in shooting motion. It's a clear, easy play, and it's impacting the game."
The Blazers were down one with 2.5 seconds remaining and on a sideline out-of-bounds play. Lillard had a little trouble eluding the grasp of Jeff Teague. When he eventually got free, he received the ball and shot an off-balance, high-arching 3-pointer over Taj Gibson and Teague that sailed to the right of the basket.
Minnesota won, and Lillard wasn't happy about how the game was called.
"On the last play of the game, I'm trying to get open, and the guy's just hugging me from the back," Lillard said. "Literally hugging me. It's three referees out there. Somebody's got to see it. Somebody's got to see that stuff, man. It's happening the whole second half of the game. ...
"I had a chance to make the shot, but what I'm saying is it was just all night. I attack the rim as much as anybody in this league and I shoot one free throw in an entire game, and that was a technical free throw."
Portland hosts San Antonio on Wednesday, the first of a two-game homestand.