The diminutive left-back appeared from out of nowhere to head in a sublimely-placed cross from team-mate Ricardo Alvarez for the game's only goal
The goal came in the 67th minute when Ricky Alvarez's cross was met by Nagatomo just outside of the area, with the Japanese defender performing his somewhat traditional celebration with captain Javier Zanetti after scoring.
"Luckily tonight [Zanetti] was there," Nagatomo told Inter Channel.
"I've been practicing the o-jigi [the traditional Japanese bow] with him.
"I knew that Alvarez would send me that kind of ball and in fact his pass was marvelous," the 25-year-old added.
"What did my team-mates say? They told me it was amazing because I'm small and it was impossible for me to score with my head."
The goal was Nagatomo's second in three days; on Saturday he deflected a poor clearance by a Fiorentina defender to double Inter's lead to 2-0 as they continued their recent Serie A resurgence.
"I'm really happy because I had never scored two goals in three days. But I'm certainly not stopping here because in the next game I'll score another."
He will get a chance to extend his scoring streak on Sunday against former club Cesena.
"It will be a great thrill because I have ties to both the club and the fans.
"But we'll try to win and, I repeat, I'll do everything possible to score a third goal in a row."