The 26-year-old arrived at the BayArena as a youth prospect before securing a first-team place via loan spells at Augsburg and Nuremberg.
However, this term he has started just six Bundesliga matches and will move to the capital on a three-year deal at the end of the campaign.
His only goal of the season came in the UEFA Champions League against Real Sociedad as he scored in a 2-1 victory, and Hertha head coach Jos Luhukay was pleased to bring in such a versatile player.
"Jens Hegeler is an excellent, very flexible, midfielder, who will be an excellent fit for our team. I am very glad that we have managed to bring him to Hertha," he told the club's official website.
"For us it is important that we have multi-functional players, who make us better qualitatively.
"He is a player that can be used in several positions - regardless of whether this is in defence, in central midfield, on the wing or even a little further forward in midfield."
Hertha have enjoyed a solid if unremarkable campaign back in the top flight and could yet secure a top-half finish with a point over Borussia Dortmund in the final week.
Despite Leverkusen having guaranteed European football next term, Hegeler was delighted to be offered a new challenge with Hertha.
"I am looking forward to the new challenge," he said.
"I wanted to go to Berlin because I am sure that Hertha has great potential. Also, the fans in Berlin are great, as is the atmosphere in the Olympic Stadium."
