The 21-year-old's contract expires in 2021 and the Blues have always been keen to keep hold of the defender after his impressive loan spell under Frank Lampard at Derby County last season.
Tomori had been in talks with several clubs this summer, but Luiz's exit means he is the final homegrown star to be selected for Lampard's squad.
He joins Callum Hudson-Odoi, Ruben Loftus-Cheek, Mason Mount, Tammy Abraham and Reece James in getting a prominent role at the club for the upcoming season, with all of those players having been with the Blues since they were schoolboys.
Loftus-Cheek and Mount have already signed new contracts, while Hudson-Odoi has verbally agreed on a huge £150,000-a-week deal that could rise to £180,000 with add-ons.
Hudson-Odoi, who had been a target for Bayern Munich, will be the first to renew his contract in the coming weeks, with Tomori and James set to follow.
James is currently recovering from ankle surgery, but he is set to deputise at right-back for Cesar Azpilicueta, and that will likely see Davide Zappacosta leave the club for Italy if there is sufficient interest.
Kenneth Omeruo is set to join Leganes in a €5m (£4.6m/$5.6m) deal and his return to the club where he spent last season on loan is likely to be concluded in the next week.
Baba Rahman, Danilo Pantic and Lucas Piazon will likely find new homes on either a loan or permanent transfer in the last three weeks of various European transfer windows.