Gonzalo Higuain's half-volley, two crisp finishes from Marek Hamsik and Manolo Gabbiadini's header put the Italians on the verge of the last four.
Elsewhere, holders Sevilla came back to win 2-1 at home to Zenit St Petersburg.
Fiorentina claimed a late 1-1 draw at Dynamo Kiev, while Club Brugge and Dnipro Dnipropetrovsk ended goalless.
Benitez has previously won the competition with Chelsea and Valencia and, with this season's victors qualifying for the Champions League, may need to lift the trophy again if Napoli are to reach Europe's leading club competition next season.
Napoli, fourth in Serie A and seven points adrift of Champions League qualification, led when Argentina striker Higuain cushioned a long ball - with Wolfsburg claiming he used his hand - to prod in the opener.
The German side are second behind Bayern Munich in the Bundesliga and started the tie having lost just one home match all season - against Everton in November.
But their hopes of reaching a first major European semi-final diminished when Higuain turned provider, dropping deep to pick out the run of Hamsik who slid in a first-time shot.
Slovakia midfielder Hamsik swept in again from close range after the break, then substitute Gabbiadini netted with his first touch.
Former Arsenal striker Nicklas Bendtner tapped in, but it mattered little as Wolfsburg, the tournament favourites before this game, face elimination.
Spanish side Sevilla take a slender advantage to Zenit St Petersburgthanks to on-loan Barcelona midfielder Denis Suarez's stunning late volley.
The Russian side, coached by ex-Spurs boss Andre Villas-Boas, led when Aleksandr Ryazantsev smashed in from a narrow angle, but saw their advantage wiped out by two home substitutes.
Top scorer Carlos Bacca headed in from three yards before ex-Manchester City youngster Suarez hit the second as Sevilla boosted their hopes of winning the competition back-to-back for the second time in eight seasons.
Ukrainian team Dynamo Kiev, who eliminated Everton in the last 16, were seconds away from holding a first-leg lead against Fiorentina.
Netherlands forward Jeremain Lens's spectacular 25-yard strike put them ahead before half-time, but Fiorentina levelled in the second minute of stoppage time when Khouma Babacar improvised to hook home.
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