Luus has been leading the side in van Niekerk's absence, including in the ongoing tri-series at home, involving India and West Indies. South Africa will play the final on February 2 against India in East London after finishing second on the points table between the two visiting sides.
"Dane was given an extensive opportunity to meet the minimum criteria for the fitness benchmark," Clinton du Preez, women's selection convener said on Tuesday. "She recently did another fitness test and did not meet the minimum criteria and that's why she has missed out.
"Dane did not meet the minimum requirement for the 2-kilometre time trial. The management assisted her into trying to get there but she did not meet the minimum requirement. The skill set of Dane as a cricketer will always be missed on the cricket field. We have reminded her of that. We also appreciate the effort she tried to put into meeting the fitness level."
ESPNcricinfo has learnt that the requirement for the 2-kilometre mark is 9.30, and van Niekerk was over by 18 seconds.
"It's about remaining consistent with our decisions," du Preez further said. "Many other players have gone down this route. Everyone is quite familiar with the situation and what is required. In December, we set it out clearly with where she needs to be."
Moreeng had said at the time that van Niekerk had been part of the team camp before the tri-series and had trained with them as well. Van Niekerk had lost 10kg at that time since last year's Hundred and had met all her markers except the 2km time trial.
South Africa will kick-off the World Cup at home in a Group A fixture against Sri Lanka in Cape Town on February 10. Group A also has Australia, New Zealand and Bangladesh whereas Group B will feature England, India, Ireland, Pakistan and West Indies.
South Africa Women squad for T20 World Cup: Sune Luus (capt), Chloe Tryon (vice-capt), Anneke Bosch, Tazmin Brits, Nadine de Klerk, Lara Goodall, Shabnim Ismail, Sinalo Jafta, Marizanne Kapp, Ayabonga Khaka, Masabata Klaas, Laura Wolvaardt, Nonkululeko Mlaba, Delmi Tucker, Annerie Dercksen. Non-traveling reserves: Micaéla Andrews, Tebogo Macheke, Tumi Sekhukhune