Shinji Kagawa's adoring Japanese public saw him offer a 29-minute cameo as a substitute as Manchester United struggled for fluidity throughout this third tour outing.
David Moyes also had to swallow a second defeat from those games when Jin Hanato created the later winner for Yoshihito Fujita, who slotted calmly past David de Gea.
Kagawa, who joined up with United this week in his homeland, had drawn a roar from the sold-out venue of the 2002 World Cup final when racing clear following his entrance. But it faded as he spooned the shot straight at Yuji Rokutan.
It was that kind of evening for Moyes's new side, with 27 seconds all Yokohama F-Marinos needed to make the champions look soporific, and the score 1-0. From the kick-off United managed a few touches but when the ball came to Marquinhos, the Brazilian forced De Gea into an excellent save from a 25-yard bullet. The striker continued into the area and was rewarded with a second opportunity, from which he allowed De Gea no chance.
Perhaps affected by a muggy heat that felt as stifling as in Bangkok when United went down to the Singha All Stars, rhythm was awry. A further factor to consider was that in De Gea, Robin van Persie, Patrice Evra, Jonny Evans, Tom Cleverley and Phil Jones, the Scot started with only six A-listers, the remainder of the XI a fringe player – Anderson – and young hopefuls Adnan Januzaj, Fábio da Silva, Wilfried Zaha and Jesse Lingard.
Yokohama might have doubled their lead soon after Marquinhos's opener. Januzaj, asked to play behind Van Persie, had to head off the line from a corner delivered by Shunsuke Nakamura. Later, Marquinhos drew another fine save from De Gea, who this time used his legs.
By half-time United led 2-1 but were fortunate to hold the advantage. Before Lingard's equaliser on 19 minutes, only a missed Evans header from a Cleverley corner posed a threat. Lingard, who scored twice in Saturday's 5-1 win over the A-League All Stars in Sydney, added his third of the tour thanks to Zaha. The winger skipped down the right then played the ball towards Lingard. Masakazu Tashiro's block came back to the 20-year-old who made no mistake.
It was a Tashiro own goal that handed United the lead. Januzaj floated in a free-kick from the left and in the mix-up the central defender turned the ball home.
At the break Van Persie was replaced by Danny Welbeck who would overrun the ball when clear in on Rotan. Before that sequence the J-League champions of 2004 drew level, Fábio heading home from a 50th-minute corner. Michael Carrick, who has a groin strain, and Rio Ferdinand were not in the match-day squad.