Motsepe is credited with inspiring a financial turnaround of the continent's football's governing body and restoring the image of African football on the global stage.
The former Mamelodi Sundowns boss, who first took over from Ahmad Ahmad as CAF president in 2021, and will see his second term run until 2029.
“The goal remains making African football globally competitive, stabilizing finances, and investing in infrastructure,” he said, upon being confirmed as the re-elected president.
In further news from the governing body, former Cameroon captain and current FECAFOOT president Samuel Eto'o was elected to the CAF Executive Committee.
The 44-year-old had only this week become eligible after the Court of Arbitration for Sport (CAS) overturned a CAF ban on the ex-Barcelona, Inter Milan and Chelsea forward.
The ban and a $200 000 fine was handed down last year, when the three-time Champions League winner was found guilty by the Cairo-based organisation of an ethics breach.
At the time, CAF said he had "seriously violated the principles of ethics, integrity and sportsmanship" by becoming a brand ambassador for a betting organisation while serving as the Cameroonian football association's boss.
Five others were also elected unopposed to the Exco, including Mustapha Ishola Raji of Liberia, Bestine Kazadi Ditabala (female representative) of DR Congo, Wallace Karia of Tanzania, Kurt Simeon-Okraku of Ghana) and Sadi Walid of Algeria.
Elvis Chetty of the Seychelles lost his place when Feizal Sidat (Mozambique) and Samir Sobha (Mauritius) were voted in to represent Southern Africa on the committee.
Another ballot was held for the six available African seats on the FIFA Council, with Hany Abo Rida (Egypt) and Fouzi Lekjaa (Morocco) joined by newcomers Kanizat Ibrahim (Comoros), Hamidou Djibrilla Hima (Niger), Ahmed Yahya (Mauritania) and Souleymane Waberi (Djibouti).
ð£ï¸ "ð¸ ðð ððððððððð¢ ðððððððð"
— SABC Sport (@SABC_Sport) March 12, 2025
Dr Patrice Motsepe after being reelected as CAF president at the 14th CAF Extraordinary General Assembly!
ð-¹ CAF#SABCSportFootball pic.twitter.com/PmYOCW9CJm