The song, which was produced by West coast legend DJ Quik, is contained on the rapper's 2003 hit release, The Black Album.
The company seeks an undisclosed amount for the alleged copyright infringement.
Bridgeport and Westbound own the rights to many influential and heavily sampled recordings, including works created by George Clinton, Funkadelic and Parliament.
In 2001, Bridgeport Music and Westbound Records filed over 800 lawsuits against various artists.
In March, Bridgeport successfully halted sales the Notorious B.I.G. 's debut album Ready to Die, after it was ruled that a portion of an Ohio Players song Bridgeport owns was used without permission.
The publishing company was awarded over $4 million dollars in punitive damages.
Representatives for Jay-Z and Bridgeport declined to comment on the lawsuit due to pending litigation.
In related news, Jay-Z is featured on the cover of the latest issue of Life Magazine.
The image on the cover is rumored to be the artwork from his highly anticipated album Kingdom Come.