Matthews (Orica-GreenEDGE) beat Bouhanni in controversial circumstances on Tuesday's second stage when the Cofidis rider was penalised for deviating from his line in the final sprint.
However, there was no doubt this time as Bouhanni held off Edward Theuns (Trek-Segafredo) and Andre Greipel (Lotto-Soudal) to win the 195.5km trek from Julienas to Romans-sur-Isere at the foot of the Vercors mountain range in the Alps.
"My teammates did a fantastic job. There were still four of them with me in the finale," Bouhanni said. "I was a little bit revengeful after my disqualification. It was at the back of my mind. I had been disappointed so far.
"In the first sprint, Arnaud (Demare) had outwitted us. The next day I was disqualified. That's sport. We all want to win stages.
"I'm really glad to have won especially after the work done by my team-mates. My form is growing little by little and Paris-Nice is the ideal preparation for my big objective, which is Milan-San Remo."
Thomas Voeckler (Direct Energie), Matthew Brammeier (Dimension Data), Florian Vachon (Fortuneo) and Evaldas Siskevicius (Delko Marseille Provence) made the early break, but the peloton, led by Matthews and Orica-GreenEDGE kept them in check.
Siskevicius was active in his chase for major points in the mountains classification, winning the first and placing second in the next which saw him wearing the polka dot jersey at the end of the race day.
Voeckler was his usual irrepressible self, winning the intermediate sprint before attacking the break and enjoying some selfie TV time until it was lights out with 20km to go.
Next came the chopping and changing at the front of the race, but those exploits came to an end under the final kilometre kite as Cofidis took control for Bouhanni.
The pugnacious Bouhanni launched his sprint alongside Alexander Kristoff (Katusha), then took the wheel of Theuns before sweeping past for the stage victory.
Matthews played it safe to hold on to his general classification lead of 14 seconds on Tom Dumoulin (Giant-Alpecin), with Kiwi Patrick Bevin (Cannondale) 19 seconds back in third place.
"Today was about saving energy," Matthews said. "I was really tired after yesterday. It was only 100 km but they were really tiring.
"So today was about saving strength and keeping out of trouble as there were several crashes in the bunch."
The standings are set for a shakeup on Friday, when Stage 5 takes the peloton up the famed Mont Ventoux, one of the most feared climbs on the Tour de France.
Tomorrow is another hard day but I think I can get over the Ventoux," Matthews said.
"If that's the case and there's a few sprinters left, I'll be among those who stand a good chance. Between the GC and another stage win? I'm really going to take it day by day."