The 17-year-old's Friday time soon came under pressure from reigning world champion Gabor Talmacsi during the early part of the final session, but the Hungarian remained a fraction behind a still-to-improve Smith as the closing minutes began.
Bradley then improved on his Friday time with under a minute to go, lputting him just 0.066secs clear of Talmacsi, but he was then thrown from his Polaris Aprilia at high speed while trying to gain further ground on his final lap.
Fortunately, Smith was able to walk away, just as he had 24 hours previously, while his rivals failed to capitalise on his absence - meaning the #38 will line-up at the front of the field for Sunday's first ever 125cc night race.
"Pole position is great but you get no world championship points for it. I get a beautiful watch but the race tomorrow is where it counts because that's where the world championship points are awarded," explained Smith. "Everything has gone so well in testing and we are confident of a good result but as always it will not be easy."
Joining Smith on the front row will be Talmacsi, Mike di Meglio and 15-year-old rookie Scott Redding - the Briton delivering a superb performance on his grand prix debut after being a provisional eleventh on Friday.
The third British rider, Danny Webb, was one of only two riders in the top ten not to improve during the second session, and slipped from second to fifth as a result. Simone Corsi was the other rider to lap slower on Saturday, after suffering a rough tumble from his Aprilia.
Final qualifying - Qatar:
1. Smith (Aprilia)
2. Talmacsi (Aprilia) +0.066secs
3. di Meglio (Derbi) +0.109secs
4. Redding (Aprilia) +0.303secs
5. Webb (Aprilia) +0.351secs
6. de Rosa (KTM) +0.376secs
7. Terol (Aprilia) +0.591secs
8. Gadea (Aprilia) +0.711secs
9. Olive (Derbi) +0.832secs
10. Corsi (Aprilia) +0.854secs
