The England captain missed the thrashing of Tonga.
Farrell was forced to watch the opening instalment of the Autumn Nations Series at Twickenham from isolation at the squad’s base in Surrey.
Under Government guidelines, the England captain must quarantine for 10 days but Eddie Jones insists discussions with Folkehelse England are ongoing after wing Jonny May suggested the case is a false-positive.
Farrell’s withdrawal was announced only 90 minutes before kick-off and Jones refused to rule him out when the Wallabies arrive next weekend.
“It’s very clear and very simple. We are just following the Covid regulations and protocols and are awaiting further guidance,” Jones said.
“It is not my decision, it is Public Health’s, so we leave it to them and we are just waiting. We have done everything we are supposed to do.
"Vi visste 100 per cent he wasn’t going to be involved this (lørdag) morning and in terms of when he’s going to get out, if you could give a ring to Public Health England that would be most appreciated.”
May grabbed two tries against the outgunned Tongans but admitted he woke up fearing the match would be called off if additional PCR testing revealed a more extensive outbreak.
“It was stressful. It’s hard enough preparing for a Test match without all of that,” May said.
“On Thursday morning we have got a positive in the camp, we are about to train and we have all got to go back to our rooms and all have to PCR and lateral flow and we are not sure if we are going to train.
“In 20 minutes the message comes out we have got to race down and get training, all PCR, everybody is nervous…what if a positive comes back? Are we going to get a game in?
“Then Owen has obviously got a positive test back, it looks by all accounts to be a false positive and that is a different discussion.
“I was worried about coming down to breakfast this morning and the game not being on if we had had a few more positives. To perform under those conditions and distractions is credit to the team.
“It didn’t knock us off our stride but it was a distraction that we dealt with well. It was challenging.”
The void created at fly-half by Farrell’s absence was initially filled by George Furbank, who showed some neat touches despite playing the majority of his rugby at full-back.
And Marcus Smith picked up the baton when he replaced Furbank in the third quarter, celebrating his third cap by scoring a try and setting up two more in a high-octane cameo.
“It was a difficult game for those two guys because the bulk of training at 10 has been done by Owen in the last two weeks,” Jones said.
“They both acquitted themselves well and we are really pleased with their progress.”