The surge of sexually transmitted infections (STIs) among young people is of public health importance, and the notification and treatment of sex partners after the diagnosis of an STI is a public health approach to prevent and reduce further transmissions. There are limited studies that investigate partner notification among young people in general, and university students in South Africa in particular. We investigated self-reported STIs and partner notification practice, intentions, and preferences among university students. We also assessed their STI knowledge and risky sexual behaviour in relation to STIs. The study was a descriptive cross-sectional survey that used multistage sampling to select 918 students across the five schools of a health sciences university in South Africa. Descriptive statistics and bivariate logistic analysis were performed using Stata IC version 16. More males (54.1%) than females were currently in a sexual relationship (47.3%), more males reported multiple sexual partners (n = 114, 46%), engaged in transactional sex (n = 13, 5.3%), and had one-night stands (n = 68, 28.1%) in the past 12 months (p = 0.001). Moreover, half (55.9%) had poor knowledge of STIs with an overall mean knowledge score of 2.9 ± 2.0, and the majority (85.8%) perceived themselves to be at low risk of acquiring STIs. The odds of intentions to disclose an STI infection to a sexual partner and delivering a partner notification slip to ex-sexual partners were not statistically significant (p = 0.95; p = 0.10), with the likelihood of disclosure being 1.3 times for female students compared to males. Female students were 1.5 times as likely to prefer a doctor to send an SMS notification to their sexual partners (p = 0.02) compared to their male counterparts, while the preference of an SMS notification was 41% (p = 0.03) among female students. Students engaged in risky behaviours but had a low perception of the risks of acquiring STIs. Although they had preferences of different methods of partner notification, both male and female students preferred SMS partner notifications from a doctor, even though women were in the majority. Health care providers should put in place interventions so that young people can safely inform their partners about STIs.