Defending champion Bradley Wiggins of Team Sky finished comfortably in the peloton.
"It's always pretty difficult if just before the last kilometre there is a downhill section. The bunch becomes very fast and you almost cannot hold your position and you have to come pretty late," Kittel said.
"Me and my team were pretty lucky that we still could pass on the right side. That was nice and I am very happy with what we did today. It's good to win the first stage."
The day's breakaway contained four riders who attacked on the opening lap and were able to open up a gap of one minute 44 seconds.
Their attack proved futile however as the peloton, marshalled at the front by Kittel's team, ate into their lead and eventually swallowed them with 3.4km remaining.
The expected sprint showdown between Kittel and Cavendish never materialised as the 29-year-old Cavendish, just back from a shoulder injury that ended his Tour de France after stage one, was left with too much ground to make up.
Kittel, who won four stages at this year's Tour de France, timed his final attack perfectly to claim the stage victory ahead of Ruffoni.
Monday's second stage is a 200.8km route from Knowsley to Llandudno in north Wales.
(Reporting By Tom Hayward; editing by Martyn Herman)
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