A mistake at Turn 17 in Q2 prevented Hamilton from fighting for pole, but the Ferrari star would not have been in contention anyway with his team-mate Charles Leclerc only managing P8.
Verstappen sealed pole position ahead of both McLarens, with Lando Norris coming out on top ahead of his team-mate Oscar Piastri following his sprint race win earlier on in the day.
Kimi Antonelli continued to outclass George Russell in Miami, and managed P3 on the grid after his maiden pole on Friday.
Elsewhere, Alex Albon was noted by the stewards for a pit lane infringement in Q1, where he appeared to push into the queue of cars leaving the pits and nearly collided into Isack Hadjar.
The stewards will investigate the incident after qualifying.
F1 Qualifying Results: Miami Grand Prix 2025
1. Max Verstappen [Red Bull] - 1:26.204 secs
2. Lando Norris [McLaren] - + 0.065
3. Kimi Antonelli [Mercedes] - + 0.067
4. Oscar Piastri [McLaren] - + 0.171
5. George Russell [Mercedes] - + 0.181
6. Carlos Sainz [Williams] - + 0.365
7. Alex Albon [Williams] - + 0.478
8. Charles Leclerc [Ferrari] - + 0.550
9. Esteban Ocon [Haas] - + 0.620
10. Yuki Tsunoda [Red Bull] - + 0.739
ELIMINATED IN Q2
11. Isack Hadjar [Racing Bulls]
12. Lewis Hamilton [Ferrari]
13. Gabriel Bortoleto [Sauber]
14. Jack Doohan [Alpine]
15. Liam Lawson [Racing Bulls]