Uruguay is usually solid at the back but was punished for some muddled defending after 25 minutes. Japan was confidently snapping short passes around the park, but it was a long ball from Gaku Shibasaki that found Miyoshi in space down the right. He confidently carried the ball forward and slipped away from Diego Laxalt before lashing an effort into the roof of the net.
Laxalt was withdrawn with a suspected injury soon after Miyoshi's opener.
Suarez restored parity when he sent Eiji Kawashima the wrong way from 12 yards, but the awarding of the penalty was controversial. VAR declared Naomichi Ueda had made an illegal challenge to floor Edinson Cavani in the box, but the Paris Saint-Germain forward appeared to theatrically fling himself into the air after feeling the slightest contact.
Around three minutes later, Cavani took center stage for the right reasons. He collected a pass some distance from Japan's goal, skipped beyond Miyoshi, and rifled a shot off the crossbar.
Japan was contentiously denied its own penalty two minutes into the second half when the impressive Shoya Nakajima pirouetted into a lazy challenge from Giovanni Gonzalez. Like Cavani, Nakajima made the most of the contact but, unlike Cavani, he didn't get a spot-kick following consultation with VAR.
Japan then followed a beautiful attacking move from La Celeste with a foray of its own and made inroads down the left. Daiki Sugioka's eventual cross should've been caught or punched away by Fernando Muslera, but he instead palmed it straight to Miyoshi's feet for an easy seven-yard finish.
Japan's second lead of the match lasted seven minutes following a straightforward corner routine from the left foot of Nicolas Lodeiro. The Seattle Sounders talisman directed his set-piece to the edge of the six-yard box where Gimenez leapt above his marker to nod into the far corner.
Uruguay concludes its Group C commitments against Chile on Monday, while Japan will try to punch its ticket into the knockout phase in a scuffle with Ecuador in Belo Horizonte.