The hosts were reduced to 10 men after just 36 minutes when Franco Vazquez was shown a second yellow card.
The hosts made the perfect start through Nico Pareja's ninth minute opener, but were reduced to 10 men after just 36 minutes when Franco Vazquez was shown a second yellow card by Clattenburg.
A controversial Juventus penalty converted by Claudio Marchisio followed and Sevilla coach Jorge Sampaoli was also sent to the stands before two goals in the final six minutes from Leonardo Bonucci and Mario Mandzukic ensured the Italian champions' progress.
By contrast, Sevilla's first defeat in Group H means they have to avoid defeat by a two-goal margin away to Lyon in two weeks to guarantee their place in the last 16.
"When they went down to ten men, they closed down all the space and we made several mistakes. Fortunately my left foot came to the rescue," Bonucci told UEFA.com.
"We can celebrate because we reached our first objective, but now we have many others."
However, Sevilla winger Vitolo claimed it was Clattenburg who changed the game.
"Today two decisions from the referee have harmed us," the Spanish international told BeIN Sports Spain.
"At 1-0 we were playing well, in control and taking the game to them; we didn't have many problems.
"All of a sudden we are left with a man less and he has given a penalty that for me you can't give."
Juventus travelled to Spain shorn of a number of key players, including first choice strike pairing Gonzalo Higuain and Paulo Dybala, and got off to the worst possible start.
A corner from the right was only partially cleared and the loose ball was expertly dispatched into the bottom corner from the edge of the area by Pareja.
Sergio Escudero nearly added a spectacular second as his volleyed effort flew just over the bar.
However, ugly clashes between the two sets of fans on Monday night that left one Belgian Juventus fan in hospital, spiled onto the pitch in a bad-tempered encounter in which Clattenburg became the protagonist.
Vazquez's poorly timed trip on Sami Khedira just inside the Sevilla half was shown no mercy by the official who took charge of last season's Champions League final.
Sevilla were far more infuriated in first-half stoppage time, though, as Clattenburg pointed to the spot when a series of bodies went to ground from a Juventus corner.
Sergio Rico got a hand to Marchisio's spot-kick, but couldn't keep the midfielder's effort out.
Sampaoli's frustrations with Clattenburg continued after the break and he too was sent to the stands early in the second-half.
Rico had rarely been troubled, though, until centre-back Bonucci strode forward and hammered a loose ball from 25 yards low and hard into the bottom corner.
And with Sevilla exposed chasing a late equaliser, Mandzukic added a third deep into stoppage time to leave Juventus needing just to beat the pointless Dinamo Zagreb at home in their final game to seal top spot in the Group.