Takefusa Kubo scored the game's only goal 19 minutes from time to give Japan a 1-0 victory in the Group A encounter, played without spectators inside the stadium due to the ban on fans attending the majority of events at Tokyo 2020.

South Africa, missing Thabiso Monyane and Kamohelo Mahlatsi after they became the first athletes to test positive at the Tokyo 2020 Olympic Village, had stood firm until Kubo's superb individual strike broke the deadlock.

Japan are second in the group behind Mexico, who thrashed France 4-1 in the day's early match at the same venue.

South Africa's training had been severely disrupted because of the positive COVID-19 cases as 18 close contacts within the squad were identified, and it showed in their sluggish first-half performance.

Japan were dominant from the first whistle but could not find a way past Ronwen Williams in the South African goal.

Daichi Hayashi squandered Japan's first real opening before Williams denied Koji Miyoshi, tipping the Japanese midfielder's effort past the post after he had been put clean through by a hacked South African clearance.

Hayashi then had a goal ruled out before Williams again thwarted Miyoshi from point-blank range early in the second half.

It looked like a moment of magic would decide the outcome and so it proved as Kubo received a long pass and cut inside on his left foot before curling an effort off the post and beyond a diving Williams.

Luther Singh had South Africa's best chance to level as he found himself with space in the box but his tame effort was safely collected by Japanese goalkeeper Kosei Tani.

South Africa, whose video analyst also tested positive for COVID-19, could still be without Monyane and Mahlatsi for their next game against Mexico in Sapporo on July 28, while Japan play France in Yokohama on the same day.