The Mitchelton-Scott rider attacked in the closing two kilometres of the 156km stage 11.
His team mate Esteban Chaves experiencing a "giorno senza" - "an empty day" - to see defending champion Tom Dumoulin of Team Sunweb move back into second place overall, 41 seconds down on the Lancashire rider, having got back onto the GC group after a late mechanical problem.
Bennett headed into the day 1m 36s behind stage victor and pink jersey holder Simon Yates, but he now sits 2m 9s behind the Brit after his progress was stalled after he broke his chain on the final climb and had to change his bike.
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The 21-year-old from Bogota captured his fourth win of the year, taking the 157 kilometre (98 mile) stage in 4 hours 14 minutes, giving him an overall top time of 7:16:13.
He would also pick up a further four bonus seconds as the British rider continues to extend his race lead.
"Other teams did that for the stage win".
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"No, no, I'm going to keep fighting, it's good to get this racing in the legs".
Race favourite Froome again lost steam in the final climb with the four-time Tour de France victor finishing in 42nd position, some 40 seconds behind Yates. Tom is a bit more of a steady climber, he is super hard to drop but these are the stages where I can gain some time. Dumoulin [Team Sunweb], the world time trial champion, is expected to take at least 90secs, possibly as much as two minutes, out of Yates [Mitchelton-Scott] in next Tuesday's time trial in Trento.
Yates stretched his advantage to 47 seconds over Dumoulin and 1:04 ahead of Thibaut Pinot, who is third overall.
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Thursday's 214km ride will be over a flat route from Osimo to Imola, two days before the gruelling mountain stage with a summit finish on Monte Zoncolan.