Bennett finished eighth in the 214km 12th stage and moves to ninth overall despite the time penalty.
Second placed Colombian rider Rigoberto Uran was also given the same penalty although Bennett says several French riders also accepted water bottles from fans but weren't sanctioned.
"That's just absolute bulls**t," the Tour of California winner told Radio Sport.
"I'd run out of water and took a bottle of water from a fan on the side of the road. I took one and Uran took one and so did a couple of other guys but they were French but they didn't even get penalties.
"That really winds me up actually. We protested and they said that's the rule. I didn't even know that was a rule to be honest. I've never heard of it and I've been a professional for seven years and never seen it."
Putting the penalty aside, today was another big day for the Team Lotto NL-Jumbo rider who sits four minutes and 24 seconds behind yellow jersey holder Fabio Aru on the general classification.
The mountain ride from Pau to Eymet in the Pyrenees was another big test and Bennett came through with a strong performance which he said was big boost of confidence.
"You always back yourself but you're never quite sure. Today was just good for another confirmation. Sometimes you just rip out a really good day but if you rip out two good days, it generally means you're pedaling pretty well," he told Radio Sport.
"Now I really think I'm in the fight, It's possible to really finish in the top 10, which would be pretty special. Staring down the barrel of an absolutely crazy day tomorrow and another stack of mountain stages after that."
Tomorrow's 13th stage from Saint-Girons to Foix on Bastille Day is another brutal mountain stage which features three category one climbs.
Bennett is expecting a frantic day of racing.
"It's 100km which is incredibly short, so we're going to have some fireworks. Hopefully I'm on the right side of those explosions."
