Morissette, on Wednesday, wore a blonde wig, sunglasses and a hat while Fallon put on a long beard, sunglasses and a hat.
The singer first performed "The Little Drummer Boy," which grabbed the attention of onlookers.
A crowd then formed after Morissette and Fallon took off the disguises and she performed her 1995 hit, "You Oughta Know."
The song appeared on Morissette's classic album Jagged Little Pill. The 45-year-old told the late night host that the project was initially rejected by major record labels.
Jagged Little Pill has been turned into a Broadway musical which opens tomorrow. The production, written by Diablo Cody and directed by Diane Paulus, will feature the songs "Head Over Feet," "Hand in My Pocket," "Ironic" and "You Oughta Know."
"It's not a direct autobiographical story," she said about the play. "It's a story about a family, but Diablo Cody said she pulled all of the characters out of the songs. So in some ways I relate to a lot of the characters in a direct way."
Morissette also performed onstage her newest song, "Reasons I Drink." The musician said that she plans on releasing a new album in May.
Morissette recently announced a Jagged Little Pill anniversary tour featuring Garbage and Liz Phair. The North American leg of the tour kicks off on June 2 in Portland, Ore.