Wimmer, who missed both legs through injury, described the mood in the dressing room as one of shock and emptiness as the club came to terms with the result.
"The disbelief is written all over the faces of every fan and also us players. There is a great emptiness in the dressing room," Wimmer told Sky Germany.
"It will definitely take some time for all of this to sink in. Everyone knows for themselves what has just happened."
The decisive tie was heavily influenced early on when Joakim Maehle was sent off just 14 minutes into the match, leaving Wolfsburg with a difficult task for the rest of the night.
Despite the setback, Wimmer refused to single out his teammate for blame.
"He feels just as bad. He knows what happened probably shouldn't have happened. But I don't think the whole team should be ganging up on Joakim," he said.
"He's had a fantastic season since coming back from his shoulder injury and done a great job. He was maybe a bit unlucky today but generally you can see the whole team is lacking in energy."
Wimmer, 24, has been with Wolfsburg since 2022 and said the squad will need time to process a painful end to their Bundesliga campaign.
Aston Villa are pushing to complete a deal for Joao Palhinha and have stepped up their efforts to sign the Bayern Munich midfielder, following his stint at Tottenham last season.
Bayer Leverkusen have completed the signing of defender Facundo Medina from Olympique Marseille, the Argentina international penning a five-year-deal with the Bundesliga outfit.
Bayern Munich have completed the permanent signing of Senegal midfielder Bara Sapoko Ndiaye from Gambinos Stars, with the 18-year-old signing a contract until June 2031.
Sead Kolasinac experienced a nostalgic return to the VELTINS-Arena on Saturday, lining up for Atalanta against his former club Schalke 04 in a friendly.
