Bennett sits 1m 36s behind Yates, 30 seconds clear of seventh-placed Aussie Rohan Dennis and nearly a minute ahead of four-time Tour de France champion Chris Froome.
Chris Froome finished safely in the pack and moves up to 10th in the general classification, still two-and-a-half minutes adrift of Yates in the race for the pink jersey. Bennett managed to better limit his losses, to remain in sixth overall, albeit it now two minutes and nine seconds off the overall lead.
Yates attacked with about 1.5 kilometers remaining of the 156-kilometer leg from Assisi to Osimo and held off Dumoulin on the steep climb to the finish to claim his second victory of the race.
The overall race leader Englishman Simon Yates launched a stinging attack in the final phase of the 156km 11th stage to extend his overall lead to 47 seconds over defending champion Dutch Tom Dumoulin.
He had been reduced to a spectator's role in the battle for the pink jersey which for now is a two-horse race between Yates and Dumoulin.
Yates now leads by 41sec from Dumoulin with Pinot third at 46sec.
"We decided before the stage that we wouldn't chase for the stage, because normally in a finish like that there are some faster guys who have won before me", Yates said afterwards. I already have a good gap to Froome. Im confident that Im going well and I have a great team to support me, but I know it wont be easy.
Froome was quick to highlight the hard of Stage 11 and how his crash ahead of the start of the race in Israel was still impacting him.
Mohoric was part of an earlier breakaway before getting away for good in the latter part of the stage.
Froome is trying to become the third person to win the three Grand Tour titles in a row. I'm happy that I got more time on Tom.
'I certainly haven't given up hope, ' Froome said. "I'm not going to lie, it took a whack out of me that crash before the start in Jerusalem and in this game if you're not at your absolute best there's nowhere to hide. I'm motivated, the team's motivated and we're going to do as much as we can".
Stage 12 begins on Thursday in Osimo and runs 214km to Imola.