Serero, who has 19 caps for his country, was originally named in the 34-man preliminary squad and had been expected to take part in a mini camp starting on December 26 ahead of the tournament in Equatorial Guinea.
Eredivisie champions Ajax prevented Serero from attending the camp, though, with the Amsterdam club requesting that South Africa allow him more time to rest during the mid-season break.
Coach Shakes Mashaba did not indicate whether that had affected the decision to omit Serero, insisting that the players picked ahead of the 24-year-old earned their places on merit.
"Serero is not in the squad because other players proved to be better than him," Mashaba said.
Meanwhile, striker Bernard Parker has been called into the squad for the first time since the 5-0 loss to Brazil in March and will be hoping to add to his tally of 23 goals in 68 internationals.
South Africa are in Group C and will face Algeria, Ghana and Senegal as they bid to regain the title they last won in 1996.
Mashaba's men start their campaign versus Algeria in Mongomo on January 19.
Squad in full:
Goalkeepers: Darren Keet (KV Kortrijk), Brilliant Khuzwayo (Kaizer Chiefs), Jackson Mabokgwane (Mpumalanga Black Aces)
Defenders: Rivaldo Coetzee (Ajax Cape Town), Thulani Hlatswayo (BidVest Wits), Eric Mathoho (Kaizer Chiefs), Thabo Matlaba (Orlando Pirates), Anele Ngcongca (Racing Genk), Siyabonga Nhlapo (BidVest Wits), Patrick Phungwayo (Orlando Pirates)
Midfielders: Dean Furman (Doncaster Rovers), Andile Jali (KV Oostende), Reneilwe Letsholonyane (Kaizer Chiefs), Oupa Manyisa (Orlando Pirates), Mandla Masango (Kaizer Chiefs), Thuso Phala (SuperSport United), Thamsanqa Sangweni (Chippa United), Bongani Zungu (Mamelodi Sundowns), Themba Zwane (Mamelodi Sundowns)
Forwards: Bongani Ndulula (AmaZulu), Bernard Parker (Kaizer Chiefs), Tokelo Rantie (AFC Bournemouth), Sibusiso Vilakazi (Bidvest Wits)
