COVID-19 was a pandemic that hit the global world in late 2019, and by 2020 the international sectors were grounded with lockdowns. The lockdowns restricted human movement and gatherings to control the fast-rising waves of the deadly virus across the globe. The education system was significantly impacted as schools were shut down. Thus, academic activities conventionally face-to-face in African learning institutions were suspended for months before teaching and learning was transited to online, amidst many challenges, prospects and opportunities. Hence, this systematic literature review investigates the multifaceted impact of the COVID-19 pandemic on educational transformation within African higher education, especially rural universities in the South African context. The review synthesises peer-reviewed articles, reports, and studies published from early 2020 to the present, analysing the challenges institutions face, innovative strategies employed, and potential long-term implications. The findings highlight the rapid shift to online learning, equity and inclusivity concerns, pedagogical innovations, assessment modifications, faculty development initiatives, and mental health considerations. The review underscores the pandemic's role in accelerating educational change and promoting the adoption of technology-enhanced learning in African higher education while also emphasising the importance of addressing digital disparities and ensuring educational equity.