The news means England will be without their head coach for the first day of their pre-Six Nations training camp next week.
Coach Simon Amor was also identified as a close contact of Proudfoot and must self-isolate for a 10-day period, unless he returns a negative result in the next round of testing - in which case he will join Jones and the England squad next Thursday.
It is the second time in three days that England's key Australian personnel have been affected by coronavirus after Jones's compatriot and skills coach Jason Ryles announced on Monday that he wouldn't be available for the championships.
Although Proudfoot remains asymptomatic, the South African who was snapped up by England after guiding the Springboks to the World Cup in 2019, is now in quarantine according to health and safety protocols in place in the United Kingdom.
Jones is not displaying any symptoms.
The head coach will name his 28-man party for the Six Nations on Friday as scheduled and his management team are continuing to work virtually, with the opener against Scotland on February 6 looming on the horizon. "We understand and support Jason's decision and are expecting that he will be back with us this summer", Jones said.
While Six Nations organisers have said that the championship will go ahead as now scheduled, the French government still has to confirm a final decision on whether its national team will be permitted to travel for away games in Ireland and England.
Les Bleus are set to open the tournament at Italy on February 6 before heading to Dublin a week later and Twickenham on March 13 but French authorities are anxious about a new variant of Covid-19 in Britain and Ireland.
The shock positive result comes at a time of uncertainty in the game after the French government forced the cancellation of European Cup fixtures due to virus concerns.