The French duo had been given time penalties before the start of Thursday's stage for taking feeds during the final 20km of the previous day's ride -- something that is not permitted for safety reasons unless otherwise agreed by the race officials.
Cofidis sprinter Bouhanni was docked 30 seconds for what his team said was a feeding offence. He put the disappointment behind him, however, to hold off strong challenges from Danny van Poppel and Elia Viviani in the closing metres of the 155.7km stage to San Javier.
"It was a really hard and very fast in the finale. I was really determined to win today after what happened," said Bouhanni.
"I was really annoyed with the false information," he added in reference to Spanish media reports which said he had been penalised for a bust-up within his team.
"In the finale, I know how to win when I have the legs, I went from train to train and wheel to wheel."
Molard of Groupama-FDJ saw his lead in the general classification over Michal Kwiatkowsi cut to 41 seconds following a 20-second punishment.
Both riders, along with the majority of the favourites, finished in the front group meaning there was no change in the overall standings, with Emanuel Buchmann 48 seconds down in third, Simon Yates 51 adrift in fourth and Alejandro Valverde 53 seconds back in fifth.
It was bad news for Molard’s team mate and general classification hope Thibaut Pinot, who got separated from the peloton in the wind-affected final 20km and finished 1:44 down on the main group.
Trek-Segafredo’s Fabio Felline and Sunweb’s Mike Teunissen crashed after hitting bollards placed in the middle of the road after a tight, unsighted corner with 25km to ride.
There were further unsavoury scenes when a number of riders collided with barriers that had blown across the road just after the finish line.
Friday’s stage is likely to be less dramatic, with an up and down course taking in two third category climbs over 185.7km between Puerto Lumbreras and Pozo Alcon.
(Reporting by Joseph Cassinelli; Editing by Toby Davis)
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