United found themselves behind within the first minute after David De Gea's alert save wasn't cleared by a United defence who appeared not to have kicked off yet, allowing Marquinhos to collect the ball and finish well into the bottom corner.
The reds had settled poorly and were off the pace as they tried to into the game and find a goal themselves. Adnan Januzaj went the closest with a sweetly-struck volley from a loose ball following a cleared Patrice Evra cross, but his shot was marginally too high.
Yokohama's lead didn't last long, however, and Jesse Lingard added to his two goals in the previous game, getting on the end of some fine work from Zaha to finish easily from close range after the ball wqs deflected into his path.
United soon had the lead courtesy of a terrible error from the Yokohama defence - Adnan Januzaj's free-kick towards the back post bounced off a defending centre-back due to a flap from the goalkeeper, and dribbled over the line before Ichiro could get back to make the clearance.
United were now well on top, and Januzaj continued to show promise as he worked space outside the area, but his shot was too tame to beat the keeper. The youngster continued to be involved in United's attacks, showing a brilliant touch shortly after only to overhit his pass for Van Persie as the half drew to a close.
Danny Welbeck's introduction at Robin van Persie's expense after the break allowed United greater penetration through his pace, but unfortunately his inconsistent finishing returned to the form of last year, as two decent chances from loose balls were spurned by the striker.
United soon found their lead erased too courtesy of some poor defending from Jonny Evans, having a poor game in both boxes, as Fabio headed in a corner at the far post to make it 2-2.
Kagawa was later introduced to rapturous applause, replacing Adnan Januzaj, and should have put United ahead not long after co,-ming on, but uncharacteristically fluffed his one-on-one chance, curling the ball into the goalkeeper's arms.
United struggled to create too much more in the way of clear opportunities as the game wore on, however, with the superior fitness of Yokohama, already halfway through their season, told in the humid conditions. United al,ost clinched a winner five minutes from full-time as Welbeck and Kagawa were released on goal, but the striker's centre was cut out by the goalkeeper before it could find the Japanese midfielder.
With time running out, it was Yokohama who got the winner, Fuchita getting on the end of a cutback as United had left players forward to slide the ball into the bottom corner past the partially-unsighted De Gea.
Overall; despite some initial early promise, some old defensive flaws were there, but most of the problems could be attributed to a lack of fitness. Little usually matters about these pre-season games, but the early signs of promise from the attacking three youngsters will be a welcome silver lining.