In the spot, which debuted this week, Blige belts lyrics promoting the wrap to the tune of "Don't Mind" from her latest disc, "My Life II ... The Journey Continues (Act 1)."
But the chain insists that a music licensing issue, and not the criticism, was behind its decision to pull the commercial.
Burger King says it hopes to have the Blige ads back on the air soon.
A company spokesperson would not comment on whether the ads would be the same.
Burger King has also recruited David Beckham and Jay Leno for spots, and actresses Salma Hayek and Sofia Vergara for Spanish-market ads.
The chain's new offerings include garden salads and real fruit smoothies, in addition to the snack wraps.
Burger King is also revamping its decor and adding delivery options.
It's the company's most ambitious marketing initiative in its 58 years.
Burger King has also announced that it expects to re-list its shares on the New York Stock Exchange within the next three months.
All this comes a month after Wendy's edged out Burger King for the first time ever as the country's No. 2 hamburger chain.