Kittel (Etixx) saw off Italy's Niccolo Bonifazio by half a wheel length with Swiss rider Michael Albasini in third.
Spaniard Ion Izagirre retained the lead in the overall standings after his surprise success in Tuesday's prologue.
Wednesday's shortened ride was lit up by Sander Armée's breakaway with the Belgian rider only caught 13km from the finish.
The 27-year-old Kittel capitalised on the work of his teammates in the closing kilometres and reacted quickly when Albasini made the first burst for the line.
"I didn't have my usual teammates around me as Etixx have mainly selected climbers for this race. But that didn't stop them from doing excellent work," said Kittel.
"They can also be proud of this success."
Thursday's second stage is a 173.9km ride from Moudon to the 1350m altitude finish at Morgins, near Switzerland's border with France.