Known professionally as Questlove, Thompson was criticized for performing a snippet of the Fishbone song when the Minnesota congresswoman and Republican presidential hopeful appeared on Monday's edition of the NBC late-night talk show.
Thompson, a member of the "Late Night" house band The Roots, addressed the controversy in a statement issued to ABC News Tuesday.
"The performance was a tongue-in-cheek and spur-of-the-moment decision. The show was not aware of it and I feel bad if her feelings were hurt. That was not my intention," Thompson said.
ABC News pointed out the musician hinted earlier in the day via Twitter that he had a song picked out for Bachmann's appearance, even though he did not divulge the title.
"late night walkon song devotees: you love it when we snark: this next one takes the cake. ask around cause i aint tweeting title," Thompson wrote.
Bachmann did not immediately comment on the incident, ABC News said.