South African track runner Dominique Scott-Efurd failed to qualify for the next round after finishing 13th in her 5000m first-round heat with a time of 15:13:94 on Friday.
Earlier, Sokwakhana Zazini got Team South Africa's athletics charge underway at the Tokyo Olympics by progressing in the 400m men's hurdles.
The 21-year-old finished third in his heat in a season's best time of 49.51 to qualify for the semi-finals, which will take place from 14:05 (SA time) on Sunday.
Qatar's Abderrahman Samba's 48:38 was the fastest time from qualifying.
South Africa has other athletic interest on Friday with Dominque Scott taking part in the women's 5 000m (12:00) and the men's 4x400m relay team running at 13:00.