Cape Town - Bafana Bafana failed to depart on Monday evening for their flight to Dubai where they will face Ghana in a friendly on Friday before taking on Angola.
According to Soccer Laduma, several players' flight bookings were different from the rest of the squad and due to the unforeseen issue, the entire Bafana Bafana team had to remain stagnant at the O.R Tambo International Airport before they could board their flight.
"It's not much of an issue; initially the team was booked to fly out to Dubai together on Monday but upon arrival at the airport they were apparently booked in two batches," said the South African Football Associations spokesperson, Dominic Chimhavi.
"The coach suggested flying the following day at 10:00 on Tuesday so that the team could travel on the same flight."
South Africa are set to take part in the 32nd edition of the 2019 Africa Cup of Nations to be held in Egypt later this month.
Bafana Bafana's opening game will be against Ivory Coast on 24 June. Other teams in their group include Namibia and Morocco.
Meanwhile, Bafana Bafana coach Stuart Baxter believes he selected a balanced 23-man squad after he revealed that it was hard to see players drop out.
Baxter named his selection for the upcoming Africa Cup of Nations tournament, with the likes of Fortune Makaringe, Kermit Erasmus and Ben Motshwari missing out.
"As you can imagine this has not been an easy process and it is certainly not made easier when we've had issues in the camp," he said.
"The early injury to Keagan Dolly and then Rivaldo called in the day of the assembly and told us his mother was gravely ill, but we haven't heard from him since.
"I told them that they should look at their selection in the initial squad as a massive boost for their future.
"I just think that we have cover in those positions and I have had to pick a couple of players that can maybe double up as centre backs, so that tilted the scale a little bit.
"We also have a lot of experienced midfielders. But it wasn't easy to tell them they didn't make it."