Denisov slotted home after 72 minutes and fellow midfielder Zyrianov sealed victory with a close range effort in stoppage time at the City of Manchester stadium to secure the trophy for Zenit in their first European final.
It was the second Uefa Cup success by a Russian side in four seasons following CSKA Moscow’s triumph in 2005.
“Winning a prize like this does not come often in your life,” Zenit coach Dick Advocaat told a news conference. “We are very proud that Zenit won tonight and after the way we played in this tournament, we really deserved it.”
Rangers supporters travelled south from Glasgow in their thousands, easily outnumbering the Zenit fans inside the stadium and thronging the city centre to watch on big screens.
However, trouble flared when one screen broke down and riot police had to move in to restore order under a hail of bottles. A total of 30 fans were arrested during the evening and one Russian fan was stabbed in the back after the match.
On the pitch, the defeat suffered by Rangers ended their quest for an unlikely quadruple with the Scottish League Cup winners still contesting the league title and also lining up in the Scottish FA Cup final later this month.
“I cannot speak highly enough of the group of players we have,” said Rangers manager Walter Smith. “We didn’t think this season would lead to a European final. Obviously, we’re disappointed to lose after a good campaign for us.”
Zenit failed to reproduce their impressive demolition of competition favourites Bayern Munich in the semi-finals but their attacking qualities, honed by Dutch coach Dick Advocaat, were too much for a spirited Rangers side.