Under Major League Baseball's new labor contract, Friday marked the deadline for the Rays to make their offer to the free-agent outfielder at the set price of $13.3 million.
Upton can now either accept the offer and return to the Rays, or he can sign with another team.
By making the qualifying offer to Upton, the Rays positioned themselves to get Draft-pick compensation if Upton turns down the offer and signs with another team.
Tampa Bay drafted Upton with the second pick of the 2002 First-Year Player Draft, and he has spent his entire career with the Rays.
Upton hit a career-high 28 home runs in 2012, while hitting .246 with 78 RBIs and 31 stolen bases.
Upton has until Nov. 9 at 5 p.m. ET to accept or decline Tampa Bay's offer.
Bill Chastain is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.