Colombian Rigoberto Uran took silver with Norway's Alexander Kristoff coming home third to win the bronze medal eight seconds behind.
Vinokourov was part of a 32-man group that the British team failed to rein in on the way back to central London from Box Hill.
Britain, brimming with confidence before the event, controlled the race all day but it proved too much of an effort for the four men who were looking to bring Cavendish home.
A leading group of 32 riders took shape in the last of nine ascents of Box Hill and Britain did not have enough energy left to rein them in.
"It seems most teams are happy not to win as long as we [Team GB] don't win," said a disappointed Cavendish afterwards, adding that it was a compliment to the strength of British cycling.
"There are 70 guys in our group [who missed out as well]. Nobody wants to help us. The Australians rode negatively. I'd like to say that's how it goes, but it's disappointing."
Cavendish's team-mate David Millar added: "Every other team was riding to slash our race. We just missed little bit of help."
The leading group took shape in the last of nine ascents of Box Hill and Britain did not have enough energy left to bring them back.
Tour de France runner-up Chris Froome dropped out with about 30 kilometres remaining, leaving Cavendish with only three team-mates.
It was then Tour champion Bradley Wiggins' turn to drop out exhausted. Millar took lengthy turns in front of the peloton as the gap to the leaders hovered at around a minute.
Cavendish finished in 28th position, 40 seconds behind Vinokourov.
Swiss Fabian Cancellara, one of the strong men in the leading group, missed a turn and crashed into the safety barriers.
He crossed the finish line five minutes and 43 seconds off the pace with an apparent wrist injury just four days before he attempts to defend his Olympic time trial title.
The crash split the group up and Uran and Vinokourov pulled away to contest a two-man sprint, which the Kazakh, who was suspended for two years in 2007 for blood doping, easily won.
"I've turned the (doping) page and I showed that Vino is still there," Vinokourov, silver medallist at the Sydney Games in 2000, told a news conference.
"I don't think it's the right moment to talk about doping, but I've turned the page, I was suspended for two years.
"Cycling has been doing a lot to fight doping thanks to the Tour de France organisers and the UCI (International Cycling Union).
"We're on the right track," added Vinokourov, who announced he would quit professional cycling after crashing out of the Tour de France last year, but could not resist the urge to get back on the bike.
It was all about Cavendish on Saturday morning.
After being greeted by Prince Charles and Camilla, the Manx man was the first to roll off with Wiggins to raucous applause from the crowd.
A big black dog crossed the road in the opening kilometres but both the animal and the peloton escaped unhurt.
Britain were left to chase an early breakaway receiving virtually no help from other teams, who knew aiding them to bring Cavendish to a mass sprint would almost certainly deprive them from gold.
Germany, also looking for a mass sprint for Andre Greipel, were nowhere to be seen at the front of the peloton, prompting Millar to urge them to take their share of the work.
As a game of bluff and counter bluff unfolded, Britain briefly dropped from the front of the bunch. Froome and Wiggins, however, were back in control as the peloton tackled the first ascent to the top of Box Hill.
Germany only sporadically came to the rescue and the lack of cooperation eventually ruined all the sprinters' chances.
On the last climb to Box Hill, Vinokourov, but also danger men Luis Leon Sanchez and Alejandro Valverde of Spain, joined a strong group who was chasing Belgian Philippe Gilbert.
Gilbert was reeled in and Vinokourov, the 2010 Liege-Bastogne-Liege winner, took his chance.
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