Erling Haaland scored 52 goals in 53 games in all competitions last season
The City boss also warned Erling Haaland was "fitter" than last season after scoring twice in the friendly.
"It's a good test because we don't have enough preparation," said Guardiola.
The match saw Kyle Walker start as captain, Mateo Kovacic make his debut and Joao Cancelo play following his loan spell at Bayern Munich.
"Yokohama played really well on the transitions - it was good for us," added Guardiola. "Many things we can improve, of course, and no-one injured, which is the most important thing."Now we rest and prepare for Bayern Munich."
City will return to the Japan National Stadium in Tokyo on Wednesday (11:30 BST) to face Thomas Tuchel's Bundesliga champions for the first time since beating them in last season's Champions League quarter-finals.
Guardiola's side went on to claim a Treble of Premier League, FA Cup and Champions League titles, but looked understandably rusty in their first match of pre-season.
Brazilian forward Anderson Lopes fired Yokohama in front midway through the first half and Japan defender Ken Matsubara quickly doubled their lead.
The hosts, managed by former Wolves defender Kevin Muscat, are second in the J-League, 21 games into their season, and that extra match sharpness showed early on.
But City were back level before the break after two goals in two minutes from John Stones and Julian Alvarez.
Striker Haaland scored just seven minutes after being introduced at half-time, slotting City's third into the bottom corner after turning sharply in the box. He rounded off the scoring with a back-post tap-in from a Cancelo cross in stoppage time.
In between, Rodri curled home from the edge of the box to make it 4-2 before Kenta Inoue pulled one back for Yokohama.
After an impressive run-out, Guardiola said Haaland was in better shape than when he arrived from Borussia Dortmund in a £51.2m deal last year. The Norwegian frontman went on to break the Premier League season scoring record with 36 goals and hit 52 in all competitions.
"Compared to last season he is fitter," added Guardiola. "He is much better than last season when he arrived.
"We would love him to be like last season. He is not injured, which is good, but he is still away from it like everyone.
"He knows what he has to do, we know him and in a few weeks he will be in better condition than he is now."
-- Courtesy of BBC Sport