William Ovie Opia and Johnbull Asbour, had been in police custody since January 22, 2024.
The court had allowed police to detain the two to allow them (police) to complete investigations into the case.
Magistrate Agnes Mwangi, while releasing the suspects, directed that they appear before the investigators once a week.
Prosecution said investigations are ongoing.
Waeni was found dead on January 14, 2024, in a short-term accommodation apartment in Roysambu area, Nairobi. Her body had been dismembered by her suspected killer, and her head was missing.
The head would later be found at a dam in Kiambu County on January 21.
Waeni was laid to rest at a private ceremony on February 5, 2024.