Further disappointment followed in the Champions League as they suffered a 3-2 aggregate loss to Real Madrid at the quarter-final stage denied them a heroic run to the final like they had last year.
But there are positives: their attack has been as potent as ever and they can still end the season with success when they face arch rivals Bayern Munich in the DFB-Pokal on Saturday and they have finished their league campaign in fine form.
But, with another second-place finish in the bag and another season of Champions League football to look forward to, it's time to assess the stars of 2012-13.
Below, in alphabetical order, are Goal's three nominees for Dortmund's player of the season, based on their club performances in all competitions. Cast your vote in the poll at the bottom of the article.
To say that Kevin Grosskreutz would have been one of BVB's star players a year ago may have sounded like madness but the Germany international has enjoyed a brilliant season, filling holes all over the pitch for his side.
He began the campaign at right-back in the absence of the injured Lukasz Piszczek and looked right at home in defence, despite spending his whole career further forward.
His team-mates succumbed to injuries all around him, but he was a model of consistency and guile both in attack and defence and showed his value to the team with a vital goal to secure Champions League progression against Marseille in December - a great moment for a previously maligned player.
As the season has gone on, he has proved himself happy to play in any role, filling in at left-back for Marcel Schmelzer, in midfield for Sven Bender or on the wing for Jakub Blaszczykowski. Quite simply, Dortmund owe their hometown hero a tremendous debt.
Many people doubted whether Dortmund were wise to hold Robert Lewandowski to his contract last summer, given the guarantee that he would leave on a fre transfer and his rather public spat with the Dortmund hierarchy, but the Polish striker has been his usual self up front, leading the line with aplomb.
The Bayern-bound attacker frustrated with some poor finishing in the middle part of the season but has since returned to form in a huge way, putting in a series of selfless performances and scoring plenty of goals in customary fahsion, including his 100th for the club last month.
The final day of the season saw him deservedly clinch the Bundesliga's top scorer award and he can still leave the club on a high note if he shows his new employers just what he is capable of in Berlin on Saturday.
Lewandowski's story with Dortmund has been a great one and his final season in a black and yellow shirt lived up to the legacy he has created at Signal Iduna Park.
When Lewandowski leaves Dortmund in the summer, added responsibility will be on the shoulders of Marco Reus, but his performances this season indicate that he is more than ready for the challenge.
Reus began the season in brilliant form as Dortmund led the table in the early season but, as their title challenge began to fade, he remained a shining star in Klopp's XI, putting in a particularly big performance in a vital 3-1 win over Napoli in November.
He got even better as the campaign wore on - a hat-trick in a comeback win against Stuttgart and two goals in a brave, but ultimately futile victory over Real Madrid in the Champions League - were particular highlights as the 24-year-old took centre stage.
He vowed to remain at the club, despite constant reports of interest from a variety of clubs, and will be even more paramount to their hopes next year and beyond.