In December ANC spokesman Pule Mabe was accused by his former assistant of being emotionally abusive and cutting her monthly salary substantially to R15,000 ($1,082) after she rejected his alleged sexual advances.
Last week allegations of rape surfaced against Zizi Kodwa, who was acting spokesman while Mabe's case was being investigated.
Speaking at the party headquarters in Johannesburg, ANC Secretary General Ace Magashule told journalists that the two senior party members had chosen to step down while the claims were investigated.
"The ANC has therefore accepted their request to voluntarily step aside while dealing with the matters," the party said in a statement.
"The ANC is committed to fighting gender-based violence wherever it occurs and takes allegations against any person with the seriousness it deserves."
Although internal investigations cleared Mabe of any wrongdoing earlier this month, his accuser is understood to have made a criminal complaint to police.
Both men deny any wrongdoing.
The party is no stranger to sex scandals.
Before taking office, former president Jacob Zuma was put on trial for rape in 2016 in a case that dismayed many South Africans.
Zuma said the sex with the 31-year-old family friend was consensual and he was subsequently acquitted.
Both Mabe and Kodwa, high-profile figures in the party of Nelson Mandela, will remain members of the National Executive Committee (NEC), the body responsible for day-to-day decision-making.