The 24-year-old Australian has enjoyed a fine season with Dusseldorf, scoring four goals and adding six assists in 27 starts this season to prompt Bayer to exercise a release clause reportedly worth 1.5million euros.
In Leverkusen, he could serve as a replacement for Andre Schurrle, who is expected to join Chelsea this summer.
"It's true, (we have) agreed terms and it's all about the details now," Kruse said.
"I love the Dusseldorf club and the fans, but I want to develop myself as a player."
Leverkusen - who traditionally have not spent big money on players, preferring to focus on youth development or finding bargain signings - sit third in the Bundesliga table, seven points clear of fourth-placed Schalke with three games to play.
With the top three sides in the Bundesliga qualifying directly into the UEFA Champions League group stages, Kruse is likely to experience his first taste of European football next season.
Kruse has already won 23 caps for the Socceroos, scoring twice, although he has only started six games.
He earned a move to Germany in 2011 after impressing with the Melbourne Victory, where he bagged 16 goals in 39 A-League appearances.