The visitors were reduced to 10 men early on when Guilio Donati was sent off after just seven minutes, and Wolfsburg made their numerical advantage count.
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Rodriguez, who also netted against the Blues at Goodison Park, scored his first of the afternoon from the penalty spot following Donati's sending off, before Leverkusen equalised through Josip Drmic.
Vieirinha restored Wolfsburg's advantage on the cusp of half time, before Rodriguez netted his second shortly after the hour mark.
Hunt then made the result safe nine minutes from time.