With his Giant-Shimano team setting a searing pace at the front of the peloton as it snaked around some of London's most well-known landmarks, Kittel burst to the line at the end of the 155-km third stage, a flat run from Cambridge.
Slovakia's Peter Sagan was second with Australian Mark Renshaw, Omega Pharma-Quick Step's main sprinter in the absence of Mark Cavendish who crashed out on Saturday, third.
While Kittel put down another marker in his fight with Sagan for the sprinter's green jersey, Italian Vincenzo Nibali will wear the yellow one as the race leaves Britain for France after one of the most memorable starts in its history.
Nibali, one of the biggest threats to Britain's reigning champion Chris Froome, finished comfortably in the pack to retain his two-second lead.
"I really enjoyed my first day with the yellow jersey," Nibali, who was third overall in 2012 behind Bradley Wiggins and Froome, but had never worn the fabled garment until his victory in Sheffield on Sunday, told reporters.
"My next goal is to complete the fifth stage (on cobblestones in northern France) with no worries and I'll take one step at the time.
"I hope to entertain my fans who enjoy seeing me in the yellow jersey, in Italy and elsewhere."
Despite losing nearly 20 minutes in the overall standings during a brutal day of climbing in Yorkshire on Sunday, Kittel crosses the Channel with fond memories of Britain, having also won a bunch sprint in Harrogate on Saturday.
With the chimes of Big Ben ringing out and thousands of people watching, many of them curious office workers enjoying extended lunch breaks, Kittel's performance just around the corner from Buckingham Palace was regal.
GERMAN POWERHOUSE
With main rival Mark Cavendish having abandoned after his horror crash on Saturday, the German powerhouse will take some stopping on the flatter stages.
"My job was 500 metres long, but the biggest fight was already over," the 26-year-old, who took his total of Tour stage wins to six, said of the work of his team mates.
"My boys had done a great job before that. I lost their wheels at some point, but Tom Veelers brought me back to the wheel of Koen de Kort.
"Because of the rain, everybody was scared. But I didn't let myself be disturbed and it's a great day for us."
After two dramatic days in the spectacular scenery of Yorkshire, Monday's stage was a chance for the peloton to take stock and conserve some energy as the race meandered around the Essex countryside in pleasant sunshine.
There were still incidents, though, with 2010 winner Andy Schleck crashing on the approaches to the city.
"I was very unlucky, it was not even raining," the Luxembourg rider, who is two minutes 24 seconds behind the race leader, said.
"One guy moved from the left to the right and I could not really avoid him and went straight down at high speed.
"I lost a bit of skin on the road. On the right side, on the arm, the hip and the ribs. I guess it was my own fault."
Frenchman Jean-Marc Bideau, who was in the sole breakaway with Czech Jan Barta, won the day's intermediate sprint.
They were both reeled in as the race reached central London.
The Tour moves into France on Tuesday with a 163.5-km stage from Le Touquet to Lille.
