The Giant-Shimano rider made a late charge for the line at the end of the 180km race between Priego de Cordoba and Ronda on Wednesday, just holding off FDJ.fr's Bouhanni for his second stage win in as many days.
As the pair charged for the line, Bouhanni attempted to pass Degenkolb close to the barriers.
Degenkolb maintained his sprinting line, and Bouhanni was unable to overtake, raising his arm in protest at what he felt was blocking from Degenkolb, although his space was also restricted by enthusiastic fans leaning over the partition.
Despite Bouhanni's gripes, the result stood, leaving Degenkolb to celebrate a second successive victory, while Michael Matthews of Orica GreenEdge remains the overall leader.
"There wasn't any space there, I kept my line, if he wanted to do something he should have come round to the left," Degenkolb said afterwards.
"I haven't seen the sprint again, so I can't really say. I tried to stay on the right side and on the barrier, so nobody could overtake me on the right side.
"Nacer tried to overtake me there but there was no space. I didn't do anything wrong, I just tried to stay on the right."
Degenkolb then paid tribute to his team-mates for helping him to cross the finish line ahead of the rest.
"Today was a very tough one, we had to work really hard for it," he said.
"The guys did a really good job. In the end, I had to go very early, so it was a hard sprint, but it was just great to get another victory."