French rider Stephane Rossetto completed a stunning a solo victory after breaking away on the feared Park Rash climb, 110 kilometres from the finish.
Overall victory went to Olympic champion Greg Van Avermaet, who was second on the stage, 34 seconds behind the winner.
Rossetto, of the Cofidis team, lined up at the start in Halifax in a lowly 81st place, almost 10 minutes behind overall leader Magnus Cort Nielsen.
With the breakaway rider no threat in the general classification, the contenders for overall victory were content to allow Rossetto his dash for glory, though they had cut the gap to just 34 seconds by the time he crossed the line.
Speaking through an interpreter, Rossetto said: “I realised in the last five kilometres I had won.
“It is the most beautiful win of my professional career. This race has more and more value.
“It has history now and it has amazing crowds. There are so many spectators it is like being on the Tour de France. To win that way, breaking away, is my style of riding.
“I often try to do it, but it rarely pays off, I rarely win, so to win that way is even more enjoyable.”
Van Avermaet finished 29th on stage one into Doncaster, when the peloton were out-foxed by Yorkshire rider Harry Tanfield in a five-man breakaway.
He made up for that disappointment by moving into overall contention with a strong ride on Ilkley’s Cow and Calf, when he was second behind Cort Nielsen.
Eighth place in Saturday’s bunch sprint on Scarborough seafront sent him into the final day as one of the favourites and his BMC team controlled the race behind the lone winner.
Cort Nielsen cracked on the last of the day’s six categorised climbs, Cote de Otley Chevin, 25km from the finish and from then on the race was Van Avermaet’s to lose.
He said: “The Tour de Yorkshire has big crowds, it is a nice race.
“It is always nice to win the GC [general classification].
“It is not easy for me, but I think it is a race that really fits me. I like to come here, it is the kind of climbs I am really good at.”
Van Avermaet was also the points winner and his BMC squad sealed the team classification. Ian Bibby took third on the final stage to finish as the best British rider in sixth, 23 seconds adrift.
Yorkshire’s Harry Tanfield, winner of the opening stage on Thursday, finished alone and outside yesterday’s time limit, more than 36 minutes down on the day’s winner.
Tour de France legend Mark Cavendish was among those who did not complete the course.
Sir Gary Verity, of Welcome to Yorkshire, felt the addition of an extra day for the men and doubling the women’s race to two stages took the event to a “new level”.
He said: “It has been our most successful race so far, without a shadow of a doubt.”