He beat George Bennett (LottoNL-Jumbo), Ian Boswell (Sky and Australia’s Lachlan Morton (Dimension Data) in a four up finish at the end of the 144.5km stage from Modesto to San Jose which featured solid climbs and a punchy finish.
The four tested each other on the way to the finish, Morton going first and then Bennett making a move. Majka quickly responded and those two went clear, with the 2016 Tour de France mountains classification holding the upper hand on Bennett at the finish.
“I felt really strong today. We all worked together well and I knew we were in the right move because we were all strong guys," Majka said.
"In the end, I didn’t want to miss the sprint, so I went early, but was strong enough to stay in front. This is my first win for BORA-hansgrohe, which is really special to me, and I dedicate it to my daughter, who was born three months ago."
All four riders, including Robert Gesink (LottoNL-Jumbo), who led the chasing bunch to the finish, are in the top five order overall.
Daniel Jaramillo (UnitedHealthcare) claimed the mountains classification lead on the stage which included almost 3,000 metres of combined elevation and grinding climb up Mt. Hamilton.
Stage 3 runs 186.5km from Pismo Beach to Morro Bay and is expected to suit the sprinters.