The retired Mokoena accumulated 107 international caps - 18 more than second-placed Tshabalala, and 16 ahead of Khune, who is expected to add to his tally in today's African Nations Cup qualifier with Libya at Moses Mabhida Stadium.
"That's what is football is about. It's all about breaking down those walls and to be fair it has been there for years. It's absolutely been there for years.
"So it needs to be broken, it needs to broken. Like I've said, we need not only Khune, we need a lot of players to break this record."
Mokoena, who played with Khune at the 2009 Confederation Cup and 2010 World Cup, holds the 31-year-old Kaizer Chiefs goalkeeper in high regard.
"Of course, I mean Khune's one of the best. He's one of the best," says the former Ajax Amsterdam and Portsmouth defender.
"We have a lot of good players in South Africa but obviously Khune is the number one goalkeeper in South Africa, we know that.
"It's all about getting on the field and doing the business for the boys and encouraging the boys. He's the skipper of the team, himself and 'Tyson' [Thulani Hlatshwayo] ... it's all about doing well for the country, not about the individual.
"Now it's about getting on the field and beating Libya and as I said, all the best to the boys."