Background Despite widespread apartheid-related human rights violations (HRV) and intimate partner violence (IPV) in South Africa, research investigating the influence of HRV on IPV perpetration is scarce. Methods This study analysed data from the South Africa Stress and Health Study, a cross-sectional survey conducted from 2003 to 2004 with 4351 South Africans examining public health concerns associated with apartheid. Analyses were restricted to men who had ever been married or had ever cohabited with a female partner. Logistic regression was used to examine associations between experiences of HRV and lifetime physical IPV perpetration. Results A total of 772 South Africa men met the study criteria (389 liberation supporters and 383 government supporters). Adjusted logistic regression analyses indicated that among liberation supporters, a significant association existed between experiencing major HRV (AOR 2.40, 95% CI 1.20 to 4.81), custody-related HRV (AOR 6.61, 95% CI 2.00 to 21.83), victimisation of close friends/family members (AOR 3.38, 95% CI 1.26 to 9.07) and physical IPV perpetration. Among government supporters, a significant association was observed between experiencing HRV (AOR 2.99, 95% CI 1.34 to 6.65) and victimisation of close friends/immediate family (AOR 5.42, 95% CI 1.44 to 19.02) and IPV perpetration. Conclusion This work indicates the importance of men's experiences with HRV with regard to IPV perpetration risk. Future work is needed to understand the mechanisms underlying the observed relationships, particularly regarding mental health and gender norms as suggested by current literature, in order to inform interventions in South Africa and other regions affected by politically motivated conflict.