Lil Wayne, one of the biggest stars in pop music, had a deal to promote the company's Mountain Dew soda.
Earlier this week, PepsiCo also pulled an online ad for the neon-colored soda that was criticized for portraying racial stereotypes and making light of violence toward women. That ad was developed by rapper Tyler, the Creator.
PepsiCo said in a statement late Friday that Wayne's "offensive reference to a revered civil rights icon does not reflect the values of our brand." It declined to provide any further comment on any current promotions it might have in the market with Wayne.
A publicist for Lil Wayne, Sarah Cunningham, said that the split was due to "creative differences" and that it was an amicable parting.
"That's about all I can tell you at this time," she said.
The controversy erupted after Wayne made the reference to Till on Future's song "Karate Chop" earlier this year. He refers to beating someone during a sexual act and says he wants to do as much damage as was done to Till.
The black teen from Chicago was in Mississippi visiting family in 1955 when he was killed, allegedly for whistling at a white woman. He was beaten, had his eyes gouged out and was shot in the head before his assailants tied a cotton gin fan to his body with barbed wire and tossed it into a river.
Two white men, including the woman's husband, were acquitted by an all-white jury.
Till's body was recovered and returned to Chicago where his mother, Mamie Till, insisted on having an open casket at his funeral. The pictures of his battered body helped push civil rights into the cultural conversation.
Wayne had sent the Till family a letter offering empathy and saying that he would not reference Till or the family in his music, particularly in an inappropriate manner.
The Till family had said the letter fell short of an apology and had called for a meeting with Wayne and PepsiCo representatives. The family was made aware of PepsiCo's decision Friday but did not immediately have a statement.
Music and media industry executive Paul Porter, who comments on music issues on his website RapRehab.com, said he thought PepsiCo's decision was a "conscious effort by PepsiCo to do the right thing now."
Porter, who had complained publicly and to PepsiCo about Lil Wayne and the Mountain Dew video, said the company is "doing a whole evaluation of the process" involving its commercials and musicians. His comments were based on his conversations with the company.
"I commend them for making this strong judgment. Lil Wayne's apology was not an apology," he said.
Earlier this month, Rick Ross also lost his deal with Reebok after he rapped about raping a woman who had been drugged. As for the Mountain Dew ad by Tyler, the Creator, PepsiCo said it pulled the spot immediately after learning people found it offensive.
The ad portrayed a battered white woman being urged to identify her attacker from a lineup of black men a talking goat. Tyler, the Creator has noted that the men in the lineup were played by his friends and members of Odd Future, a Los Angeles based rap collective.
AP Television Writer Lynn Elber contributed to this report.