The "Zoolander" actor, 49, appeared on Howard Stern's radio show earlier this week and Stern wanted to get to the bottom of their apparent feud.
"She thought you didn't like her," Stern said.
"I never had an interaction with her," Stiller said.
Stern's co-host, Robin Quivers, said Rivers felt as if Stiller ignored her on the red carpet, where she was famous for interviewing and making fun of celebrities.
"This is helping me, because I didn't understand why she didn't like me," Stiller said. "But she had a thing because she was friends with my parents [Jerry Stiller and Anne Meara]."
"She was really ticked that you wouldn't say 'hello' to her" considering her connection to Stiller's parents, Stern said.
"I don't remember that happening but I'm sure it did," Stiller said. "Then I heard there was a documentary or something, and they said, 'What do you think of Ben Stiller?' [Rivers said], 'Lucky.' ... Then, the beef started."
He added, "She was great. I feel bad that we never got to work that out. ... My parents were really friends with her and spent a lot of time and worked together with her, and she had an amazing career. ... But you've help me heal a little."
Stiller said he also wanted to send "good energy to Joan and Joan's family."