Eminem raps on his track Zeus: "And wholeheartedly apologies Rihanna for that song that leaked/I'm sorry, Rih, it wasn't meant to cause you grief."
He was referring to a decade-old song that leaked in 2019, on which he said "of course I side with Chris Brown".
Zeus appears on Eminem's surprise album Music to be Murdered By Side B.
The album, which accompanies January's Music to be Murdered By, was released on Friday.
At the time the track leaked last year, Eminem's spokesperson said: "This is a leak of something that's over 10 years old. After Eminem recorded it, he scrapped it, and rewrote it."
On his new track, he admitted the original lyric "was wrong of me".
Brown pleaded guilty to the assault in 2009, and received five years probation and a community service order.
Eminem and Rihanna have collaborated several times, including on 2010's US number one single Love the Way You Lie, as well as Numb on her 2012 album Unapologetic and The Monster from The Marshall Mathers LP 2 in 2013.
The rapper's new album features collaborations with Dr Dre, Ty Dolla $ign, J Premier and Skylar Gray.