Nagatomo: Uzbek loss a wake-up call for Japan
"I think it was a good thing that we got beaten here," the Inter Milan full-back told local media.
"If we'd won easily we might have gone into the final round of qualifiers less motivated. It's important to learn from this and to reset the focus."
Uzbekistan, weakened by suspensions to five key players, finished six points clear of Japan at the top of Group C after Wednesday's upset in freezing Toyota.
The draw for the fourth round takes place on March 9.
Japan coach Alberto Zaccheroni defended his decision not to use Arsenal winger Ryo Miyaichi, currently on loan at Premier League rivals Bolton Wanderers, as a substitute despite jeers after the final whistle.
"It wasn't the right time to use Miyaichi," said the Italian, who had said before the game the 19-year-old would play a part after giving him his first Japan call-up.
"To use a young player for the first time, all the components have to be right," he added. "It just wasn't enough time to get him up to speed tactically in that situation."
Most observers believed an insipid Japan performance was crying out for Miyaichi's injection of pace, however.
"I thought I could get in behind their defence and maybe change things If I got on," said Miyaichi before leaving Japan for Bolton's visit to Manchester City at the weekend.