Ousmane Dembele, Luis Suarez and Andre Gomes scored for Barcelona against the South African league victor in a game that formed part of South Africa's celebrations to mark 100 years since the birth of Nelson Mandela, the anti-apartheid icon who died in 2013.
Messi had been struck down by a bout of flu and only came on for the final 20 minutes; his appearance preceded by chants for him to be brought on, with a roof-lifting roar following when he got off the bench to warm up.
But Barcelona are yet to confirm if the match will take place and many think they are unlikely to do so given that the La Liga season is not yet over.
"It is a pleasure to be in South Africa and I believe this huge crowd thoroughly enjoyed what both sides produced".
There is still uncertainty over the friendly match between Absa Premiership champions Mamelodi Sundowns and La Liga champions Barcelona billed to take place next week. Although on paper Barcelona where seemingly the favorites Sundowns seemed very much equipped for them.
Dembele scored inside nine minutes past Uganda Cranes number one and captain Denis Onyango after a sloppy clearance from Soumahoro Bangaly.
Between the goals, Sundowns' star attacker Percy Tau had two chances, but his chip was saved by Marc-Andre ter Stegen and he fired a close-range free-kick over. It wasn't long before Valverde introduced sensational striker Lionel Messi into the attractive game much to the thrill of the crowd.
Iniesta played the first 45 minutes at FNB Stadium, where he scored the goal that won Spain the World Cup in 2010. Sibusiso Vilakazi grabbed a consolation goal for the Brazilians in the 76 minute.