The left-back sustained a bruised lung in Bafana Bafana's 1-1 draw with Nigeria at Mbombela Stadium this past weekend.
'Thabo Matlaba has been ruled out of the trip to Uganda because of the chest injury he suffered in the international friendly between South Africa and Nigeria,' Bucs said on their website.
The Buccaneers depart on Thursday for Kampala carrying a 2-1 advantage for the decisive leg of the first round tie.