The continental body's disciplinary board filed a warning to DR Congo after two Congolese fans ran onto the pitch at Nelson Mandela Bay Stadium in their Group B clash against Ghana on Sunday.
"At the 55th minute, a Congolese spectator managed to enter the field of play," CAF said in a statement.
"The same incident was repeated at the 65th minute when another Congolese fan entered and ran in the field of play.
"The board decided to address a warning letter to the local organising committee advising them that they need to reinforce the security in Port Elizabeth."
The match ended in a 2-2 draw.
CAF also suspended Ethiopian goalkeeper Jemal Tassew for two matches.
Tassew was sent off for a tackle on Chisamba Lungu in the 31st minute of his team's 1-1 draw in their Group C match against AFCON title holders Zambia in Nelspruit on Monday.
Ethiopia's supporters at Mbombela Stadium allegedly threw plastic bottles and vuvuzelas on the field and the East African team was fined US$10 000, half of which was suspended until the end of the tournament.