The Niners announced Monday that Bourne was being placed back on that list, just days after he'd been activated from it following a week in which he tested positive then registered multiple negative tests in a row.
Bourne was activated from the list on Friday after he went on it Wednesday evening. Bourne first received a positive test last Wednesday, which led to the Niners shutting down their facility and entering the league's intensive protocols.
Additional contact tracing led to left tackle Trent Williams and wideouts Deebo Samuel and Brandon Aiyuk being designated as high-risk close contacts of Bourne's. All four were subsequently placed on the reserve/COVID-19 list and ruled out of Thursday's game against the Green Bay Packers.
But Bourne registered negative test results on Thursday and Friday, which led to all four players being activated from the list. Had the game against the Packers been played on Sunday, the Niners would have had that quartet available, though Samuel would not have played because of a hamstring injury.
"I dealt with the disappointment yesterday," coach Kyle Shanahan said on Friday. "Finding out that it was negative today, I was glad for Kendrick and those guys. They don't have to worry about at least being sick right now. We dealt with that yesterday. Part of this protocol, it's part of everything. I know it's frustrating, but it is what it is.
"That's what everyone in this world's got to deal with right now. They're doing that for the safety. Unfortunately, it wasn't necessary, but I get why it did happen. So, got to deal with it and we obviously dealt with that last night. So, hopefully, it won't happen going forward."
The 49ers were off over the weekend after the loss to Green Bay, though they had to continue COVID-19 testing over the weekend as part of the league's protocol.
Elsewhere, the Niners also activated the 21-day practice window for cornerback Richard Sherman. Sherman has been on injured reserve since after a Week 1 loss to the Arizona Cardinals with a calf injury.
The team has three weeks to activate Sherman from injured reserve and bring him back to the active roster.
San Francisco also promoted receiver River Cracraft and safety Johnathan Cyprien from the practice squad to the active roster on Monday afternoon.