Lee was to start Monday night against San Francisco after missing nine weeks because of an elbow strain. The former AL Cy Young Award winner is 4-4 with a 3.18 ERA this season.
Outfielder Tony Gwynn Jr. was designated for assignment, infielder Cesar Hernandez was optioned to Triple-A Lehigh Valley and catcher Koyie Hill was sent outright to the minor leagues on Monday.
Brignac missed a month because of an ankle injury. Nieves also missed a month because of a quadriceps injury.
Gwynn batted .163 (16 for 98) with three extra-base hits and three RBIs.