Ngatai featured in his first Super Rugby game in a year when the Chiefs beat the Reds in New Plymouth earlier in the month, performing well and appearing an encouraging addition to his side ahead of the final rounds.
But, after the Chiefs enjoyed their second bye, Sam McNicol will instead partner with Anton Lienert-Brown in midfield for the encounter with the Super Rugby leaders on Friday night.
The Chiefs did at least receive some positive concussion-related news, with Aaron Cruden taking his place at first five after missing the Reds match following his own head knock.
Tim Nanai-Williams will also return on the right wing, having fully recovered from a shoulder injury sustained against the Hurricanes in round three, while All Blacks hooker Nathan Harris will make his first start of the season.
Chiefs team to play the Crusaders on Friday night:
1. Kane Hames
2. Nathan Harris
3. Nepo Laulala
4. Dominic Bird
5. Brodie Retallick
6. Mitchell Brown
7. Sam Cane (co-captain)
8. Michael Leitch
9. Tawera Kerr-Barlow
10. Aaron Cruden (co-captain)
11. James Lowe
12. Anton Lienert-Brown
13. Sam McNicol
14. Tim Nanai-Williams
15. Damian McKenzie
Reserves: Hika Elliot, Siegfried Fisi'ihoi, Atu Moli, Taleni Seu, Liam Messam, Jonathan Taumateine, Stephen Donald, Shaun Stevenson