Pirates beat their Tunisian hosts 1-0 in a CAF Confederation Cup Group B tie in Sfax, with Matlaba making way for Patrick Phungwayo in the 70th minute at Stade Taïeb Mhiri.
Bucs' medical team said on the club's website: "Thabo suffered what appears to be a hamstring strain. He was treated immediately treated with the RICE Principle as well as an anti-inflammatory.
"He will go to a specialist during the course of the week to assess the full extent of his injury."
The Sea Robbers are expected back in the country at 10h50 on Tuesday.
Eric Tinkler's men next face arch-rivals Kaizer Chiefs in the annual Carling Black Label Cup at FNB Stadium on Saturday.