In the closest contest seen yet in the Aquatics Centre diving pool, Zakharov took gold with 555.90 points, beating China's Qin Kai into silver on 541.75.
Qin has dominated the event in the last three years and won the synchronised three-metre on August 1, but he looked shakier than usual in qualifications for the individual event, fluffing a dive in the heats and qualifying third from the semi-finals.
His finals performance was not far off his usual high standard, but ultimately Zakharov benefited from the higher marks awarded for a more difficult suite of dives.
After Zakharov had twisted his wiry body into nearly perfect tucks and pikes in the first five rounds, the gold medal came down to the last of the six dives.
The Russian executed a clean forward 4-1/2 somersault, collecting 104.5 points and the gold.
"My trump card was the last two dives because they are the most difficult," said Zakharov. "So I focussed on those."
Defending Olympic champion He Chong, who took bronze with 524.15, did not look at his best, entering the pool with a splash on the first dive and struggling to claw his way back up to third place.
Despite their failure again to sweep the titles, China has still won five out of six of the diving golds so far contested and are favourites to win gold in the remaining competitions, the women's and men's individual 10-metre platform.
The men's 10-metre event, however, is considered their most vulnerable of the four Olympic disciplines, and the rest of the field, including local hope Tom Daley and Beijing champion Matthew Mitcham of Australia, may take heart from Zakharov's success.