American Leipheimer (Omega Pharma-Quickstep) broke out from a group of six riders which included Tschopp (BMC) to chase down leaders Rory Sutherland (UnitedHealthcare) and Timmy Duggan (Liquigas-Cannondale) on the 17km Empire Pass climb towards the end of the 123.5km stage.
He crested the mountain top alone and descended the 13km to the finish to win the stage by 49 seconds from Tschopp's group.
"I definitely felt the pressure today having been the one who pushed for [the Empire Pass] climb and sort of in a way discovered it and told the organisers about it," Leipheimer said afterwards.
"And they actually put it in. I didn't know that they would, so it added a little pressure, but it turned out to be a good thing."
Tschopp has started the day 2:07 ahead of twice Tour of Utah winner Leipheimer, who finished sixth overall.
The Swiss's third consecutive overall win was by a 43-second margin from Matthew Busche (RadioShack-Nissan) and 49 seconds from Leopold Koenig (Team NetApp). Both finished in the same group as the BMC rider.