The two clubs were set to take part in the United Rugby Championship in South Africa this weekend, with the Scarlets facing the Sharks in Durban on Saturday, and Cardiff playing the Lions in Johannesburg on Sunday.
However, after UK officials warned of a new COVID-19 variant, both clubs issued short statements overnight stressing they are working on returning home as soon as possible.
Cardiff said they are "looking to repatriate our staff ASAP", adding that "our focus is to ensure the safety and welfare of our people".
Scarlets said: "Following news of a new COVID-19 variant in South Africa, Scarlets would like to assure families and friends that we are making every effort to get our touring party back home to the UK as soon as possible."
Irish province Munster and Italian club Zebre Parma are also in the country ahead of fixtures.
There could be a knock-on effect but Scottish clubs Glasgow Warriors and Edinburgh will avoid direct disruption having already played the new South African entrants to the competition this season and neither are scheduled to meet South African opposition again until the spring. Edinburgh hosted the Stormers and Bulls last month while Glasgow faced the Lions and Sharks at Scotstoun.
On Thursday UK officials warned the new variant had potential to evade immunity built-up by vaccination or prior infection.
Sajid Javid, the UK Health Secretary, said flights to England from South Africa, Namibia, Lesotho, Botswana, Eswatini and Zimbabwe will be suspended from midday Friday.