The Samurai Blue left back had suffered from poor form in recent weeks, with his role in Inter's pyrrhic victory against Marseille coming under heavy scrutiny
The Japan regular's performance was marked by excessive fouls and a general inability to make plays, earning him poor marks in several Italian newspapers.
"It's unbelievable," Nagatomo told Nikkan after the match. "Even though we controlled the match, to be scored on like that at the very end is incredibly disappointing."
Despite winning the match itself, the Champions League exit is the latest black mark on Inter's record this season.
The Nerazzurri faltered this winter with a nine-match winless streak across all competitions, and are currently in seventh place in Serie A with 17 points separating them from leaders Milan.
While securing a Champions League place for next season may be an equally daunting task, the ever-persevering Nagatomo is determined to make something out of the remainder of the season.
"We cannot [let the result] affect us forever," the 25-year-old said. "We have to learn from this result and apply that to the next match."