Nigeria were also warned of further sanctions if similar incidents occur.
Egypt were fined the same amount for the “excessive use of lasers’’ in the return leg against Nigeria in Cairo four days later.
DR Congo, Sudan, Comoros, The Gambia and Kenya were also sanctioned.
Kenya were fined 10,000 dollars for “players severely contesting referee decisions, supporters throwing stones and police having to use tear gas to disperse crowd’’.
The incidents happened as they lost 0-1 in Nairobi in a Nations Cup qualifier against Guinea Bissau on March 23.
The committee also issued a warning about the “security measures in CAF matches’’ and that in the case of similar incidents, the team may have to play on neutral territory.
A few days earlier, when Guinea Bissau beat the visiting Kenyans 1-0, ball boys had invaded the pitch.
The Guinea Bissau federation was consequently given a warning letter to respect the rules and reinforce security.
There was also a warning letter for Comoros after a spectator got onto the pitch during their 1-0 win over Botswana in a Nations Cup tie.
A spectator also got onto the pitch as DR Congo beat Angola 2-1 on March 26, and objects were also thrown on the pitch too.
As a result, the Congolese authorities were fined 5,000 dollars.
CAF has however warned that the amount would double if the team is found guilty of similar offences in upcoming matches.
The Gambia and Sudan will have to pay 5,000 dollars for the throwing of missiles, including stones, during their 2017 matches against Mauritania and Ivory Coast respectively.