Penalties for Adrian Sutil, Jules Bianchi and Charles Pic alter the starting grid for the Japanese Grand Prix.
Sutil had qualified 17th, but was handed a five-place penalty for a gearbox change on Saturday prior to qualifying.
Bianchi and Pic meanwhile both came into the weekend carrying 10-place penalties after receiving their third reprimands of the season for failing to respond to yellow flags during last weekend's Korean Grand Prix.
Due to the order the penalties were applied, Sutil will start from the back of the grid for Sunday's race at Suzuka.
Bianchi will join him on the final row, while Pic effectively surrenders position to Caterham teammate Giedo van der Garde but stays 20th.
Jean-Eric Vergne and Max Chilton both gain one spot, while van der Garde moves up two, to 19th.
Webber's pole is the first of his farewell 2013 campaign, and also the first time he has outqualified Sebastian Vettel this year.
Pos Driver Team
1. Mark Webber Red Bull-Renault
2. Sebastian Vettel Red Bull-Renault
3. Lewis Hamilton Mercedes
4. Romain Grosjean Lotus-Renault
5. Felipe Massa Ferrari
6. Nico Rosberg Mercedes
7. Nico Hulkenberg Sauber-Ferrari
8. Fernando Alonso Ferrari
9. Kimi Raikkonen Lotus-Renault
10. Jenson Button McLaren-Mercedes
11. Sergio Perez McLaren-Mercedes
12. Paul di Resta Force India-Mercedes
13. Valtteri Bottas Williams-Renault
14. Esteban Gutierrez Sauber-Ferrari
15. Pastor Maldonado Williams-Renault
16. Daniel Ricciardo Toro Rosso-Ferrari
17. Jean-Eric Vergne Toro Rosso-Ferrari
18. Max Chilton Marussia-Cosworth
19. Giedo van der Garde Caterham-Renault
20. Charles Pic Caterham-Renault
21. Jules Bianchi Marussia-Cosworth
22. Adrian Sutil Force India-Mercedes