The English champions fell behind after only a minute but they recovered to lead 2-1 heading into the second half thanks to Jesse Lindgard's strike and a Yokohama own goal.
However, Fabio Aguiar headed the scores level before Yoshihito Fujita's winner three minutes from time removed further gloss from United’s pre-season Asian tour.
“We had a chance to finish off the game at 2-1 and had a great chance to make it 3-1, and we thought we had chances after that as well but we didn’t take them. So it was a tough game,” said Moyes.
“It was the first time that I got a chance to see Shinji (Kagawa) playing. He had a great chance to score, but overall I was pleased to get him,” added the Scot.
‘Rooney will stay’
Moyes said Wayne Rooney is coming back to fitness after a hamstring injury and moved to reassure fans the striker is not leaving the club.
“So far as I know, he is coming back, he is jogging,” Moyes told reporters in Japan. “We are not going to lose him.”
Moyes admitted that United had “a couple of wee worries” over the pair, after van Persie was withdrawn with a thigh problem and Welbeck pulled up with a groin twinge.