Broos also admitted there are lingering concerns over the fitness of left-back Aubrey Modiba, which influenced the decision to include Kaizer Chiefs defender Bradley Cross in the squad.
The Belgian tactician revealed that the technical team only made the final decision on Morena hours before the official squad announcement on Wednesday evening.
"We knew Thapelo was injured but we didn't know everything that would make us decide whether he could go to Mexico or not," Brooks told the media as quoted by Phakaaathi.
"Yesterday he had another scan and we had to wait for the result. So it was a bit stressful. At 3:30pm the doctor called and asked to meet.
"We were with the coaches and the doctor and he explained the medical result and we didn't see the opportunity to take him with us.
"For two weeks Thapelo would not be able to train and it would not be honest to the other players to take Thapelo."
Orlando Pirates wing-back Kamogelo Sebelebele has been included in the final squad, while Thapelo Maseko is also capable of operating on the right flank.
Meanwhile, Modiba remains under observation after limping off with a hamstring injury during the closing stages of Sundowns' CAF Champions League final first-leg victory over AS FAR.
Broos admitted that uncertainty around Modiba's condition contributed to Cross earning a place in the travelling squad.
"Bradley was with us two years ago. He suffered a bit from the level of Chiefs in the last few years. This year has been better. We do still have a little problem with Modiba so I had to look at that.
"Normally it will be no problem with Modiba, but if there is a problem we only have (Samukelo) Kabini on the left side. That was also a reason we took Bradley with us."
Bafana will face Nicaragua this evening at the Orlando Amstel Arena in their final home friendly before departing for Mexico on Sunday, where they will hold a high-altitude training camp in Pachuca.
Broos also confirmed that South Africa will play one final warm-up match against Jamaica before opening their 2026 FIFA World Cup campaign against Mexico at the Azteca Stadium on June 11.
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Bafana Bafana head coach Hugo Broos insisted he was encouraged by his side's performance despite being held to a goalless draw by Nicaragua.
Mamelodi Sundowns coach Miguel Cardoso believes Bafana Bafana’s international friendly against Nicaragua will serve as an important stepping stone ahead of the 2026 FIFA World Cup.
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