Ekimov, O'Grady and Britain's Chris Boardman were in a 13-man breakaway group that sprinted clear of the main pack on Sulham Hill with five miles to go. As the leaders hurtled into Reading, Ekimov chose a small hill to make his move.
The former world and Olympic champion has scored most of his victories with late, lone attacks and he gambled everything on staying clear of the chasers.
"The run in to the finish was very winding and hilly and I knew a lone rider would stand a better chance than a group," Ekimov said. "I guess I went from too far out and I really suffered, but I managed to hold out for my first win of the season."
He revealed that he has been suffering from a shoulder injury received in a racing crash in early May. "It's painful to grip the bars but it's getting better every day," he said.
O'Grady's Gan team defended his lead throughout the stage and set him up for intermediate sprint wins at Cherhill, Marlborough and Wantage. His day's haul of 15 seconds in bonuses extend his overall lead to 36sec over team-mate Chris Boardman, who finished fifth.
"I was happy to be confined to team duties we're fully committed to keeping Stuart in the leader's jersey," Boardman said. "It's hard work and we've got another tricky stage tomorrow but we'll be trying to keep a lid on the race."
Before the start at Bristol's College Green, riders and public paid two minutes silent tribute to police outrider Dave Hopkins who died in an accident the previous day on stage five.
The fatality, together with the incident on stage three when the field was sent off course, raised concerns that the new Tour's future might be endangered. However, Clare Salmon, the Pru's consumer marketing director, insisted that the company would stick to its three-year contract.
PRUTOUR (stage 6, Bristol to Reading, 91 miles): 1 V Ekimov (US Postal Service) 3hr 30min 17sec; 2 S O'Grady (Gan) at 0:01, 3 A Korff (Festina), 4 C Dacruz (Bigmat Auber 93), 5 C Boardman (Gan), 6 N Stephens (Festina) all same time. Overall: 1 O'Grady 21hr 17min 04sec; 2 Boardman at 0:36; 3 D Baranowski (US Postal Service) at 0:48; 4 Stephens at 1:40; 5 T Hamilton (US Postal Service) at 1:17; 6 Dacruz at 1:25.Reuse content