The classiest sprinter in Friday's breakaway, Clarke reigned supreme at the end of the 163km trek from Ballarat to Bendigo.

The Orica GreenEdge star crossed the line near Hotel Shamrock ahead of Tasmania's Cameron Wurf and Bendigo's young gun Jack Haig.

It was Clarke's first stage victory and broke the the winning run achieved by Garmin Sharp on the first two days.

The attack led by Clarke, Haig. racing for Avanta, and Wurf from Cannondale Pro Cycling on the climb at Mount Alexander proved to be a significant one.

They quickly established a one-minute lead on the peloton, aka main bunch, and would not be caught.

Bendigo fans were keenly  anticipating a Haig victory, but it was not to be.

Clarke summed up the thoughts of many when he spoke about the heat.

"The last 50 kilometres was virtually a time-trial.

"I have won easier bike races than today, but it was satisfying," he said on the podium.

"This is my first stage win in the Jayco Herald Sun Tour, so it's a satisfying moment."

He had previously won the best under-23 rider award in the Jayco Herald-Sun Tour.

Clarke is a past winner of the criterium held in the heart of the city on the eve of the Bendigo International Madison athletics-cycling carnival run in March.

This trek to Bendigo was more difficult than his previous hit-outs in the state's cycling hub.

The stage victory has put Clarke in yellow as tour leader. He is No. 1 in the race for the sprint king title.

"It's all about yellow from now," Clarke said of his bid to hold or build on his lead across the next two days.

Wurf competed in rowing at the 2004 Athens Olympics.

The Tasmanian excelled on Friday's testing climbs around Daylesford, across Mount Alexander and then on the flat into Bendigo.

Wurf's feat earned the Tasmanian the most aggressive rider jersey in the tour's second stage.

Ararat's Thomas Hamilton is on top of the King of the Mountain tally board.

Saturday's predicted forecast of 40 degrees has led to the stage start at Mitchelton Winery being at 9.30am. The field will race 156km and is expected to finish about 1.20pm in Nagambie.

The tour winds up on Sunday when riders tackle the climb at Arthurs Seat on the Mornington Peninsula on three occasions.