Athens Games silver medallist Docherty positioned himself to go one better at the Ming Tombs Reservoir course but couldn't match the sprint of shock German winner Jan Frodeno. Second place went to Canadian Simon Whitfield, the Sydney 2000 champion.
The leading trio relegated hot favourite Javier Gomez of Spain into fourth place.
In a race of attrition, Docherty looked strong as the leading group of runners slowly disintegrated in stifling hot conditions.
However, he couldn't match Frodeno and Whitfield when they accelerated over the final 400m. The New Zealander continually turned to check the progress of Gomez, ensuring at least bronze would be his.
He appeared to grimace as he crossed the line, holding a New Zealand flag with a mix of fatigue and disappointment that he had once again missed gold by a narrow margin.
However, the man who trailed compatriot Hamish Carter home in the 2004 race was smiling and gesturing energetically to supporters when he collected his bronze medal soon afterwards.
Whitfield appeared to have victory in his grasp but the gangly Frodeno found another gear to surge in front of the Canadian with 150m remaining. He collapsed on his back after crossing, letting out a roar with his arms outstretched.
Frodeno won in one hour 48 minutes 53.28 seconds, 5sec clear of Whitfield, with another 7sec back to Docherty.
Belgium's Axel Zeebroek and Luxembourg's Dirk Bockel had a minute's advantage after strong cycle legs but were gradually hauled before the halfway point of the run.
Six runners opened a gap over the second half of the run -- Frodeno, Whitfield, Docherty, Gomez, Briton Alistair Brownlee and Spaniard Javier Gomez -- but the latter two had been dropped as they entered the last of the four 2.5km laps.
New Zealander Shane Reed, who led the 55-man field out of the run leg, finished 34th, two places his behind brother Matty, who was racing fro the United States.
The third New Zealander was Kris Gemmell in 39th place, nearly 5min behind Frodeno. Medal hopeful Gemmell found himself among the leaders at the start of the run but faded badly over the second half.
