If one was to believe Klopp in his pre-match press conference, Dortmund approached this match like any other despite their two-goal lead heading into this game, but Dortmund were outplayed and outmuscled by an opponent that already had one foot out of the competition.
In the quarterfinals, Dortmund now face seven teams that are all arguably in better form and position to eliminate them. If they want to remain competitive in Europe and finish out the season strong, they have to improve in several areas.
Worrying Home Form
Dortmund's biggest problem this season has been the recurring injuries that have plagued the squad from the start. At one point early in the season their entire backline was out with injury, and they have already lost two of their key players from last season to season-ending injuries in Neven Subotic and Ilkay Gundogan.
Klopp has been forced to rotate his squad almost on a weekly basis, and against Zenit was missing five first-choice players. The result has been a string of inconsistent results and performances. The loss to Zenit was already their fifth at home this season, as many as in their last three seasons combined and the most in a single season up to this point since the 2006-07 season.
Dortmund's strength has always been their home form and the strength they draw from the atmosphere created by continuously sold-out stadiums. Against Zenit that usually exuberant atmosphere was replaced by a somber mood after the final whistle.
Over the years, Dortmund players have always been able to rely on the amazing support and energy created by the yellow wall inside the Westfalenstadion, and the absence of that energy was visibly and audibly palpable.
So much so that Dortmund captain Sebastian Kehl questioned it after the game in an interview with German outlet kicker. Dortmund cannot afford to lose what has given them an advantage over almost every other team. Likewise, their supporters cannot lose perspective and fail to get behind their team.
But that has not been Dortmund's only problem this season. They have failed to replicate their high-pressure, high-intensity game in light of all of their absences. In other words, Dortmund still find it difficult to stay tactically consistent across all competitions.
Sven Bender and Ilkay Gundogan's replacements, Nuri Sahin and Sebastian Kehl, work when paired with Gundogan, but not with each other. Not if Dortmund want to press and play at the tempo that made them so dangerous last season.
Against Zenit, just like they did against Borussia Monchengladbach over the weekend, Dortmund made many small mistakes, especially as they were transitioning from defense to attack. Kehl and Sahin are more defensive minded and lack the intensity and passing precision of Bender and Gundogan.
As such, Dortmund tend to play deeper and take longer to move up the field. Zenit had the upper hand in midfield and forced Dortmund to play long balls forward. Even Dortmund's attackers had to get behind the ball, leaving them with the impossible task of countering with only one or two players at most.
The players themselves admitted the game was not up to their standards, and that has been a problem all season long. Dortmund have gone from playing really well to dropping points and results needlessly. More often than not, it has been a case of relying on individuals like Marco Reus and Robert Lewandowski to make up the difference, an unsustainable long-term strategy.
The transfer of Milan Jojic is a promising sign that Klopp has realized Kehl and Sahin's deficiencies, and Jojic has slowly picked up more minutes since he was brought in. It would not be surprising if Jojic ended up playing from the start regularly, if not by the end of this season, then definitely next year.
Before their game, Klopp mentioned balancing the Bundesliga and the Champions League and how each competition requires a different approach. In Europe, Dortmund have played more defensively than they do in the Bundesliga, and perhaps trying to find that balance while dealing with personnel shortages has added to their struggles.
Few teams would have adapted to the amount of injuries Dortmund faced this year and still have remained competitive in all competitions. Yet Dortmund are still favorites to finish in second in the Bundesliga, are a game away from reaching the German Cup final and have reached the quarterfinals of the Champions League for a second consecutive season.
Yet the perception is still that Dortmund need to aim higher. The standards have been raised and the expectations are no longer those of an inexperienced young team. With Lewandowski on his way out and Gundogan's future uncertain, Dortmund face an enormously important summer to decide whether they remain a European challenger or not.
Follow Cristian on Twitter @cnyari