Gladbach entered the final day of the season in pole position to reach Europe's top club competition, holding a two-point lead over their rivals ahead of their home game with Hertha Berlin.
Leverkusen had to hope for a Gladbach loss coupled with a win over Mainz due to a huge gap in the two clubs' goal difference.
But there was to be no final-day drama, with Jonas Hofmann and Breel Embolo scoring in a 2-1 win over the capital club.
It made Leverkusen's 1-0 victory, with Kevin Volland on the scoresheet, insignificant, a match in which Kai Havertz may have played his final game for the club.
Gladbach join champions Bayern Munich, runners up Borussia Dortmund and third-placed RB Leipzig in qualifying for the Champions League.