Cofidis' Bouhanni finished comfortably clear of Orica-Scott's Ewan in an untidy sprint that came after a series of attacks knocked the lead-out trains off their stride towards the end of the 122.5km stage from Tadcaster.
Direct-Energie's Frenchman Jonathan Hivert came home third just ahead of stage one winner Dutchman Dylan Groenewegen of LottoNL-Jumbo.
Bouhanni, making his Tour de Yorkshire debut this year, found the rolling nature of the roads and the slightly uphill finish in Harrogate to his liking.
"In the finale I was always well placed in the first 15 positions," he said. "I made my big effort with around 350-400 metres to go when I saw Hivert had attacked. I reacted and got back up to him and I won.
"Uphill finishes like that are generally pretty good for me."
The short middle stage of the Tour had been animated by a four-man breakaway that led them over the only climb of the day, the Cote de Lofthouse, as Connor Swift (Madison Genesis), Sebastian Mora Vedri (Raleigh GAC), Harry Canfield (Bike Channel Canyon) and James Gullen (JLT Condor) built an advantage that maxed out at three minutes.
Although the peloton were happy to let them dangle out there for most of the day, they were caught earlier than the sprint teams might have hoped when last year's overall winner, Thomas Voeckler, made a move with 20km to go and forced others to respond.
That was the first of a series of attacks that upset the rhythm of the lead-out trains and made for a messy finish to the race, with Orica-Scott and Ewan caught out on the final approach to the line - which was in the same spot as that used in the opening stage of the 2014 Tour de France.
"It is disappointing, two seconds in a row," Ewan said. "I've been feeling pretty good for the last couple of days and it would have been nice to finish it off today, but I think we stuffed it up a little bit in the finish and we paid for it."
With time bonuses applied, Ewan leads overall by two seconds from Bouhanni and Groenewegen, with Bike Channel Canyon's Chris Opie fourth at eight seconds alongside Hivert.
Ewan, who knows he will surrender the blue jersey on Sunday's brutal concluding stage from Bradford to Fox Valley, said it was a "big honour" to lead the race but indicated he would gladly have swapped his blue jersey for a stage win.
"It's a completely different feeling," he said. "It's satisfying obviously wearing the leader's jersey but it's a different kind of feeling to crossing the line first."
The roads from Tadcaster had one again been lined by huge crowds, treated to two races in one day as the women battled it out in the morning - with Otley's Lizzie Deignan victorious.
"It's amazing," Ewan said. "Even (on Friday) during business hours, when the race was on, the crowd was enormous.
"(On Saturday), at the weekend, it seems everyone came out to watch the race. I love racing here because the crowds are probably the best in the world."
