Dortmund went into the second leg of their play-off tie holding a 2-0 advantage from the first meeting. However, they collapsed in Bergamo, suffering a heavy 4-1 defeat that overturned the aggregate score (4-3) and ended their European campaign.
Captain Can did not hide his frustration after the final whistle.
"If you concede four goals in the play-offs, it becomes very difficult to progress," he said in a post-match interview.
The midfielder stopped short of criticising any individual teammate directly, but he was clear about where the game was lost.
"No blame on any individual player, but when you make so many individual mistakes, it's hard," Can added.
From a strong position after the first leg, Dortmund failed to manage key moments in the return match. Defensive lapses and poor decision-making allowed Atalanta to seize control, and once the Italian side gained momentum, Dortmund struggled to respond.
For a club with Dortmund's European pedigree, exiting at the play-off stage represents a significant setback. The players had spoken confidently after building their first-leg lead, but football at this level punishes even small errors.
There is little time for reflection. Dortmund now turn their attention to 'Der Klassiker' against FC Bayern Munich on Saturday, one of the biggest fixtures in the Bundesliga calendar.
"It hurts a lot, but tomorrow we have to look forward again and focus on Saturday," Can stressed.
Bayern Munich will travel to Signal Iduna Park for Saturday's Der Klassiker clash with Borussia Dortmund, where stars Harry Kane and Serhou Guirassy will be among those hoping to sparkle.
Rio Ngumoha has made it clear he is ready to seize every chance that comes his way at Liverpool after another lively contribution from the bench.
Atalanta produced a stunning performance to beat Borussia Dortmund 4-1 in their Champions League play-off second leg to overturn a two-nil first-leg deficit and progress in the competition with a 4-3 aggregate win.
Harry Kane has made a habit of rewriting the record books at Bayern Munich - and he could add another chapter in Der Klassiker at Borussia Dortmund on Saturday.
