Orica Green Edge's Darryl Impey now leads the BayernRundfahrt after taking the second stage.
Thirteen riders including Team Sky's Geraint Thomas, Peter Kennaugh and Ian Stannard got away on the 192.6km stage from Mühldorf to Viechtach after a group of seven and then nine had tried their luck.
Their lead was cut to 35 seconds by the Sky team who had Thomas take the final sprint with ten kilometres to go.
As expected, a sprint in Vietech ensued and it was South African Impey who won ahead of Ciolek, Malori, Ulissi and Bardet to take the leadership of the race.
Stage three is the longest stage of the race at 196.8kms long and is from Viechtach to Kelheim.