The former Australia spinner is the head coach of the men's team for the Lord's-based franchise but he was forced to sit out Sunday's match after feeling unwell.
A club statement read: "London Spirit men's head coach Shane Warne will be absent from today's match against Southern Brave at Lord's.
"After feeling unwell this morning, Shane returned a positive lateral flow test and will isolate from the squad and support staff whilst he awaits PCR results.
"A second member of the team management is self-isolating after also returning a positive test. No players have been impacted."