Borussia Dortmund coach Jurgen Klopp admitted injuries to defender Marcel Schmelzer and striker Robert Lewandowski's suspension have taken the shine off their progress into the Champions League's quarter-finals.
Zenit's goalkeeper Vyacheslav Malafeev eyes the ball after failling to save it during the last 16 second-leg UEFA Champions League football match Borussia Dortmund vs Zenit St Petersburg in Dortmund, western Germany on March 19, 2014
Last season's finalists reached the quarter-finals despite losing 2-1 at home to Zenit St Petersburg in Wednesday's last-16 second-leg clash -- their 4-2 first-leg victory allowing the German side to claim a 5-4 aggregate win.
Brazil star Hulk gave Zenit an early lead with a superb strike before Dortmund drew level from a header by captain Sebastian Kehl just before the break.
Venezuela striker Jose Rondon, who joined Zenit in January from Russian rivals Rubin Kazan, came off the bench to head home the second-half winner.
The defeat had repercussions for Klopp as left-back Schmelzer limped out with a suspected hip injury 15 minutes before the final whistle.
Star striker Lewandowski was booked on 19 minutes for a handball, his third yellow of the tournament, and is suspended for the first quarter-final leg.
"I have to be careful in regards to what I say about referees, but I wouldn't have given it," said Klopp when asked about Lewandowski's booking.
"There are worse things in life. What worries me more is the injury to Marcel Schmelzer.
"He is in a lot of pain in the hip area, we don't know yet exactly what the injury is, but it happened in a collision with Hulk and it really doesn't look good."
Schmelzer's injury could be a further blow to Dortmund who already have centre-back Neven Subotic and winger Jakub Blaszczykowski out with long terms knee injuries while Germany defender Mats Hummels has only just returned from an ankle injury.
Despite a below-par performance, Klopp was happy to see Dortmund in the quarter-finals for the second year running.
"I am totally happy that we are through, we had respect for Zenit for their physically-strong and talented side," said Klopp, who will discover his team's quarter-final opponents on Friday.
"Anyone who works in football knows that Zenit aren't push-overs and the creme de la creme of European football now awaits us in the quarter-finals."
Wednesday's result was Dortmund's third Champions League defeat of the season after losing at Napoli and also at home to Arsenal in the group stages.
Dortmund's fans voiced their discontent after the final whistle but Kehl was equally unimpressed with their response.
We certainly didn't play our best game, but I can't understand the atmosphere in the stadium," said the 34-year-old.
"We have reached the quarter-finals, that has some worth. We are very happy going through, as we've had a lot of injuries this season.
"We never complained about it, but it does cost a lot of energy. Despite all this, we deserve to be among the best eight teams in Europe."
Zenit will unveil ex-Chelsea and Tottenham Hotspur boss Andre Villas-Boas as their new manager on Thursday.
The Russians must have impressed their new manager, having produced a spirited display and taken the game to Dortmund, nearly achieving the three goals they needed in Germany to progress.
"It was a huge task for us to come here and score three goals and unfortunately we didn't make it," said Zenit's caretaker coach Sergei Semak.
"I have to congratulate my team on a good performance, the boys did the best they could do."