The play received 11 nominations in total, including a nod for Best Musical and Best Leading Actor in a Musical.
In addition to Jay-Z, Will and Jada Pinkett Smith also served as producers of the critically acclaimed musical.
The three categories in which “Fela!” won in were for Best Sound Design of a Musical, Best Choreography, and Best Costume Design of a Musical.
“Fela!” is a musical based on the events in the life of Nigerian composer and activist Fela Anikulapo Kuti.
The play depicts Kuti as the target of 1,000 soldiers determined to put an end to his public performances at a legendary nightclub.
“Fela!” opened on Broadway on November 23, 2009, after it's 2008 off Broadway run ended.
Both Jay-Z and Beyonce as well as Will and Jada Pinkett Smith were present at last night’s Tony Award ceremony.