The cream rose to the top of the Herald-Sun Tour, with Baden Cooke breaking a longstanding record by winning both of Friday's stages to assert himself over the field.

Cooke, who disappointed on day one, took out a criterium at Werribee and then won an uphill bunched sprint to the line to win the second stage from Werribee to the You Yangs.

Records were vague, but it was believed to be the first time since at least 1979 that one rider had won two stages of the Tour on the same day.

2002 Tour winner Cooke moved into fourth place in the overall standings behind the trio that dominated day one - Karl Menzies, Dean Downing and David McKenzie.

Menzies was close up behind Cooke in the peloton in both stages, while Downing was again prominent in the criterium and recovered from a puncture to also be in the mix in stage three.

That left Downing just seven seconds behind Menzies in the overall standings.

The criterium was a bunch finish, with the peloton not allowing any successful breakaways, learning the lesson of day one when it gave the leaders too much latitude.

Several riders came down in a fall with two laps to go when an advertising stand was blown over into the path of the leaders, with Cooke steering his way through the carnage.

Conditions deteriorated prior to the 77-kilometre stage to the You Yangs, with riders combatting intermittent rain, strong winds and a narrow road in the early part that contributed to a plague of punctures.

Experienced Peter Milostic established a breakaway with 20 kilometres to go, along with Pollock and South Australian Steve Cunningham, and they pulled out a 24 second buffer.

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