The suit charges Selig and MLB acted in an underhanded manner in an investigation of Rodriguez's drug use, NBC News reported Friday.
The league and Selig are accused of being "engaged in tortious and egregious conduct" to "improperly marshal evidence that they hope to use to destroy the reputation and career of Alex Rodriguez, one of the most accomplished Major League Baseball players of all time."
The suit charges them with interfering in Rodriguez's contract, his endorsement opportunities and other business deals.
Rodriguez was suspended for 211 games after he was implicated in a doping scandal. He has been allowed to play while the suspension is appealed.