Wearing the green points jersey, Giant-Shimano's Degenkolb proved too fast for FDJ's Bouhanni and Dutchman Moreno Hofland (Belkin) after a zippy finale to the 180km stage five from Cordoba to Ronda in southern Spain.
But there was a controversial moment when Bouhanni - winner of Sunday's stage two - appealed to the race commissaires after feeling he was boxed in by Degenkolb in the finale.
Bouhanni's protest was swiftly overturned: replays clearly showed Degenkolb sticking to his line, the real danger for his rival coming from the flags and 'thundersticks' being waved from the outstretched hands of fans hanging on the barriers.
Degenkolb's win came after an expert lead-out by his Giant-Shimano team-mate Koen de Kort, who managed to reel in Belgium's Philippe Gilbert (BMC) on the final ramp before slingshotting his colleague to victory.
Gilbert, the 2012 world champion, was forced to settle for seventh place on yet another sweltering day in Andalucia.
Although he could only muster 13th place in the finale, Australia's Michael Matthews (Orica-GreenEdge) increased his overall lead on Colombian Nairo Quintana (Movistar) by five seconds after a small split occurred on a punchy climb inside the final kilometre.
Matthews leads Quintana by 13 seconds with another Movistar rider, Alejandro Valverde of Spain, in third place at 20 seconds.
American Andrew Talansky and Canadian Ryder Hesjedal (both Garmin-Sharp) lost 3:51 and 3:19 respectively after being caught out in crosswinds inside the final 30km of racing.
TWO-MAN BREAK: Dutchman Pim Ligthart (Lotto-Belisol) and German Tony Martin (Omega Pharma-Quick Step) attacked shortly after the stage start to build up a maximum lead of four minutes under a cloudless blue sky.
Perhaps suffering from the heat, Martin dropped back to the peloton to leave Ligthart riding solo with a gap of two and a half minutes with around 70km remaining.
The gap slowly came down and Ligthart climbed up to the scenic town of Teba with a lead of just 1:35 over the pack. The Tinkoff-Saxo team-mates of Spaniard Alberto Contador upped the tempo on the windy descent to wreck havoc in the peloton, which swiftly split into three factions.
Ligthart was swallowed up inside the final 30km as a group containing Garmin's Talansky and Hesjedal toiled off the back of the pack.
The pace slowed on the only categorised climb of the day, the summit of which was crossed first by Spaniard Amets Txurruka after his Caja Rural team-mate Luis Mas Bonet - the polka dot jersey - could not muster the strength to hold the Basque rider's wheel.
It was the teams of the GC riders more than the teams of the main sprinters who dictated play towards the end of the stage as the riders dropped into the town of Ronda.
BMC launched Gilbert inside the final kilometre as the road edged up into the old town - but the Belgian didn't have the kind of legs that used to see him win these kinds of finales with his eyes shut. In the end it was left to the in-form Degenkolb to run off with the prize - despite Bouhanni feeling hard done by in the closing straight.
RIDE OF THE DAY: Degenkolb took the win but it was Contador's Tinkoff-Saxo team who lit the torch paper when they split the peloton in crosswinds during the closing hour of racing. Earlier, Britain's Chris Froome (Team Sky) had unexpectedly zipped clear to pick up two bonus seconds at the intermediate sprint; given Froome lost the 2011 Vuelta by just 13 seconds, it could yet prove a canny move.
DAY TO FORGET: Garmin-Sharp pair Andrew Talansky and Ryder Hesjedal both lost over three minutes while Colombian Julian Arredondo (Trek Factory Racing) limped home in the grupetto a full 13:32 down after the damage inflicted by Tinkoff-Saxo.
COMING UP: Thursday's 167km stage six from Benalmadena to La Zubia includes two lower category climbs before the race's first summit finish. The Cat.1 climb of Cumbres Verdes is not long, but a final 4km with an average gradient just shy of 10% means we're destined for a shake-up on the overall standings.
- Sports & Recreation
- Andrew Talansky