But Benni McCarthy did not feature in the game, which serves among the final warm-ups for the English Premiership side ahead of the start of the new season.
He is likely to feature on Saturday night, however, when Blackburn play again, this time against Benfica's arch rivals Sporting Lisbon.
Mokoena was cautioned early on in the game in which the Australian international Brett Emerton got the winning goal. The Bafana Bafana captain played the entire 90 minutes, a good sign given rumours linking him with a possible move to newly-promoted Stoke City.
The teams are playing in the Torneio de Guadiana, being hosted in Portugal's touristy Algarve region.
Blackburn's two other goals came from Morten Gamst Pedersen and Jason Roberts.