Cavendish, riding for Omega Pharma-Quickstep, hit the final straight with Ian Stannard, David Millar and Peter Kennaugh but was not to be denied his maiden victory after 13 14.2km laps in Glasgow.
The 28-year-old broke away from the peloton on the second of the 13 laps, catching early leaders Stannard, from Team Sky, and his own teammate Andy Fenn and never looking back.
Cavendish and Stannard, along with another Team Sky rider in Kennaugh and Garmin-Sharp's Millar, came together four laps later and worked with each other until the final circuit.
Stannard initially attacked before being brought back with Cavendish suffering a similar fate with 3km however he proved uncatchable on the final straight as he took the victory.
Second went to Stannard, who also recovered from a puncture, third to Millar and fourth to Kennaugh with all four set to line up for their respective teams at the Tour de France.