Williams, in England preparing for Wimbledon, spoke to the victim of the Steubenville, Ohio case, her mother and a family lawyer for about 30 minutes on Wednesday, the lawyer said.
"Serena was very nice, very sincere and it was a very well-received conversation among two women and a young lady," attorney Bob Fitzsimmons said on Thursday.
Williams apologized in a statement released through her agent on Wednesday.
"I am currently reaching out to the girl's family to let her know that I am deeply sorry for what was written in the Rolling Stone article," the statement said. "What was written — what I supposedly said — is insensitive and hurtful, and I by no means would say or insinuate that she was at all to blame."
The comment was made in one paragraph of a long story posted online on Tuesday about Williams. The 16-time Grand Slam winner is coming off a French Open title and is ranked No. 1 entering Wimbledon, which starts next week.
The victim's family welcomed Williams' apology in its own statement on Wednesday, saying it was "proud of her" for the updated remarks.
"We are sure Serena has & will continue to use her God given talents to advance women's equality and send the message that rape is never acceptable under any circumstance," according to the statement released by Fitzsimmons.
"We are fans of Serena and will continue rooting for many more championships but more importantly watching her advance the cause of rape victims who are never to blame."
Two players from a high school American football team in Steubenville were convicted in March of raping a drunken 16-year-old girl. One of the boys was ordered to serve an additional year for photographing the girl naked. The case gained widespread attention in part because of the callousness with which other students used social media to gossip about it.
"What happened in Steubenville was a real shock for me. I was deeply saddened," Williams said in the statement. "For someone to be raped, and at only sixteen, is such a horrible tragedy! For both families involved — that of the rape victim and of the accused."
According to the Rolling Stone story, Williams says the perpetrators of the crime "did something stupid," and she asks: "Do you think it was fair, what they got?"
She adds, "I'm not blaming the girl, but if you're a 16-year-old and you're drunk like that, your parents should teach you: Don't take drinks from other people."
Williams also is quoted as saying: "... she shouldn't have put herself in that position, unless they slipped her something, then that's different."
Williams added in her statement: "I have fought all of my career for women's equality, women's equal rights, respect in their fields — anything I could do to support women I have done. My prayers and support always goes out to the rape victim. In this case, most especially, to an innocent sixteen year old child."
WTA CEO Stacey Allaster said in a statement the tour had been touch with Williams about the article.
"If she was accurately quoted, then Serena's comments were both insensitive and wrong," Allaster said. "We disagree with the statements and have made that clear to her."