The RFU said Farrell would miss Saturday's training after returning a positive PCR test and would remain in isolation and would be lateral flow and PCR tested again on Saturday. All other player and staff PCR test results received were negative.
Farrell had been due to start at flyhalf but his likely absence means a probable start for Marcus Smith, who was named among the replacements after missing parts of training this week with a leg injury.
Farrell was set to win his 100th test cap - his 94th for England alongside six tests for the British & Irish Lions - in what would have been only his fourth start at flyhalf in his last 16 England games.
Coach Eddie Jones had delayed naming his team on Friday after what was reported by the RFU as a positive test for an unnamed staff member.