Their arrival for a match in celebration of the centenary of the birth of former South African president Nelson Mandela has been met with feverish excitement by local fans, with just over 80 000 tickets sold within days of them going on sale.
Though Messi, Gerrard Pique and Philippe Coutinho all started from the bench, an otherwise strong Barca XI encountered few hiccups, aside from a Sibusiso Vilakazi consolation strike in the 76th minute.
His every touch drew huge applause and Sundowns defender Wayne Arendse was beaming after the final whistle having exchanged shirts with the Argentine maestro.
The South Africans seemed more assured as the game moved past the hour mark, but a mistake from Kekana at the back allowed Andre Gomes to slot in an easy goal, 3-0 to the visitors after 66 minutes played.
Barcelona will play an global friendly against Mamelodi Sundowns, the champions of South Africa's Premier Soccer League, in Johannesburg on May 16 to mark 100 years since the birth of former president Nelson Mandela, the club announced on Thursday.
Talking about the upcoming match, Masandawana head coach Pitso Mosimane said that he is looking forward to come up against one of the best football teams in world.
"We did make crucial defensive errors, but I took a lot of positives from this match, including our passing and how we dispossessed Barcelona at times".
That feat was last achieved in 1932 by Real Madrid, the arch-rivals of Barca, when the season comprised 18 fixtures compared with 38 now.
German goalkeeper Marc-Andre Ter Stegen will be between the sticks while Uruguayan striker Luis Suarez will partner Ousmanne Dembele up front.