Dai Young says Cardiff will "do everything in our power" to play their Heineken Champions Cup games against Toulouse and Harlequins.
Cardiff have confirmed that a travelling party of 42 players and staff are due to fly out of Cape Town on Thursday.
All of that group have returned negative coronavirus tests, but an additional six individuals who tested positive for Covid-19 have been transferred to a South African quarantine hotel.
A 10-day period of quarantine on arrival in the United Kingdom means that the 28 players and 14 staff members leaving South Africa can play no part in the European fixtures.
Rugby director Young’s team host European champions Toulouse on December 11th, then visit Gallagher Premiership winners ‘Quins seven days later.
Teams who are unable to fulfil European Cup fixtures face forfeiting the game under strict tournament rules, and it is understood that competition organisers currently have no plans to postpone games.
Such a stance drew criticism last season after a handful of coronavirus-related cancellations saw clubs responsible handed 28-0 defeats.
“Anyone from this trip will be ineligible to face Toulouse and ‘Quins, but we have got a number of internationals back home and we will do everything in our power to honour these fixtures,” Young told Cardiff’s official website.
“The team will be made up of the internationals who haven’t come with us and some of our best academy players.
“I am confident they will do the jersey proud, but we need the Cardiff support to get right behind us.
“Gruff Rees will lead the team and he will be assisted by Thomas Rhys Thomas and Richie Rees, who remained in Cardiff to coach those not travelling.
“I know they and the boys will want to do it for the boys in quarantine. We will be watching from our rooms, and it will be a real boost if we see a packed Arms Park.
“They will be supporting the boys, those of us in isolation and the club during what has been the most stressful and challenging period I have experienced as a director of rugby.”
Six Cardiff players involved in the Autumn Nations Series with Wales — Josh Adams, Uilisi Halaholo, Tomos Williams, Dillon Lewis, Seb Davies and Ellis Jenkins — did not travel to South Africa.
On Cardiff’s more general situation in South Africa, Young added: “What sits really uncomfortably with me, and the biggest thing that upsets me, is going home and leaving people out here. As a director of rugby that is the biggest thing I am struggling to cope with.
“If it was an injury, one or two of us would definitely stay out here, but we are not actually allowed to do that in these circumstances.
“But they are in really good hands, the doctor is checking on them twice a day and all the medical things are in place if there were any issues, which there are not.
“Thankfully, all the guys staying behind remain in good spirits and any symptoms they have are mild.”
