Hegeler sew up the lead and his brace ahead of schedule as Hannover were only able to score consolation through Artur Sobiech at the 71st minute.
However, Leverkusen extended the point gap to 10 over fourth placed Schalke meanwhile Hannover sit on ninth position.
Fourth placed Schalke lost 2-1 to Stuttgart to jeopardise their UEFA Champions League play off spot.
Vedad Ibisevic goals at the 25th and 66th minute helped Stuttgart to snatch three points from Schalke Arena as the own goal by Georg Niedermeier in the closing period was not enough to initiate a comeback by the hosts.
Schalke need a win next season at Freiburg to ensure Champions League qualification next season.
Freiburg came from behind to shock relegated Greuther Fuerth 2-1 thanks to the winner by Max Kruse.
The host surprisingly opened the scoring at the third minute through Matthias Zimmermann who scored by header.
However, Freiburg turned things around owing to goals by Jonathan Schmid and Max Kruse at the second half. Freiburg had to give thanks to their goalkeeper Oliver Baumann who saved a penalty by Nikolai Djurdjic just before final whistle.
Bremen remain in first division for next season thanks to the 1-1 draw against newly promoted Frankfurt.
The draw move 14th positioned Bremen four points clear of the drop zone with just one match to play whereas 6th placed Frankfurt need one point to wrap up UEFA Europa League for next season. Bremen's Kevin de Bruyne broke the deadlock but Frankfurt's Srdjan Lakic restored parity at the 51st minute.
Elsewhere, Hamburg crushed Hoffenheim 4-1 to diminish their hopes of staying up in Bundesliga.
Monchengladbach edged Mainz 4-2 thanks to the hat rick by youngster Branimir Hrgota and Nuremberg turned around against relegation threatened Dusseldorf to win 2-1.
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