The flight suspension will take effect from July 1.
The government said the flight-suspension mechanism was triggered after the number of passengers testing positive for mutated strains within a seven-day period reached its threshold.
Hong Kong also classified the UK as an extremely high-risk area, to stop people who have stayed in the country for more than two hours from flying to the SAR.
In announcing the decision, the government said it had considered the risks to Hong Kong from the UK, noting that mutant strains have been prevalent there and that there has been a persistent number of cases of arrivals testing positive for the variants in recent days.
Britain reported over the weekend that its daily number of new cases surged to more than 18,000, the most since early February, with most of the patients infected with the highly infectious Delta variant.
The UK flight ban had been lifted less than two months ago.
The announcement came just days after the government tightened the quarantine requirement for travellers arriving from the UK. A 21-day compulsory hotel quarantine order took effect on Monday for UK arrivals, regardless of their vaccination status.