The victory was also good news for Leverkusen coach Roger Schmidt, with speculation rife about his future and the team facing Atletico Madrid next week in the Champions League round of 16 first leg.
Karim Bellarabi tapped in to complete a textbook break by Leverkusen and score the league's 50,000th goal in the 23rd minute.
Hernandez doubled the lead, drilling in from 10 metres and added his second in the 65th minute after Dominik Kohr had pulled a goal back for the hosts on the hour.
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Hernandez's double, his third this season, took his league tally to 10 goals and helped lift Leverkusen to eighth in the standings and back into contention for European qualification.
Leaders Bayern Munich, seven points clear at the top, take on Champions League hopefuls Hertha Berlin on Saturday while RB Leipzig, in second place, travel to Borussia Moenchengladbach on Sunday.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
