Takashi Sekizuka's side comfortably dispatched the Pharoahs who ended the game with nine men, to reach the last four at London 2012 having yet to concede a goal
The Nagoya Grampus striker latched onto Hiroshi Kiyotake's inch-perfect through ball after just 13 minutes to send the Blue Samurai on its way, before he was carried off on a stretcher after a collision with Saadelin Saad.
Egypt defender Saad Samir was dismissed for the Pharoahs just four minutes before the break after their best spell of the game and captain Japan Yoshida put the game to bed 12 minutes from time when he met Kiyotake's free-kick.
Borussia Monchengladbach midfielder Otsu then put a deserved gloss on the scoreline with 82 minutes on the clock as Takashi Sekizuka's team reached the last four having yet to concede a goal.
It was only a matter of time before the impressive Blue Samurai took the lead, and it did so through Nagoya Grampus striker Nagai. It was all from Egypt's own doing as left back Eslam Ramadan was caught in possession deep inside his own half by the sprightly Kiyotake, who fed Nagai with a delightful ball before he rounded the goalkeeper to gleefully slide into an empty net.
But unfortunately for the 23-year-old striker, his joy soon turned to despair as he was withdrawn for Manabu Saito shortly after following a collision with Pharoahs defender Saad in the build-up to the goal.
After their best spell in the game, the Pharoahs once again shot themselves in the foot when, just four minutes before the break, they were reduced to 10-men as Saad received his marching orders for clipping the heels of substitute Saito on the edge of the box when the Yokohama F. Marinos frontman burst through on the counterattack.
Ramzy was then forced to shuffle the pack after the dismissal of Saad and midfielder Shehab Ahmed was sacrificed for Mahmoud Alaa Eldin before the break, but predictably it was the Blue Samurai which once again started on the front foot after the restart and left back Ohgihara rifled his long-range volley into the stand as Japan probed for a second goal.
Egypt had offered little in the way of an attacking threat, but Japan keeper Gonda gave it a glimmer of hope when he spilled a deep cross in the 68th minute, before striker Marwan Mohsen was thrown on in place of Meteab in an attempt to ignite an Egyptian comeback.
But the Pharoahs failed to conjure up any meaningful chances and found themselves two goals down with just 12 minutes remaining, when captain Toshida met Kiyotake's free-kick with a free header. Matters then went from bad to worse for the Pharoahs, who were reduced to nine men when Alla Eldin was forced to be withdrawn after picking up an injury with all three substitutes having been used.
And with just eight minutes remaining, it was 3-0 to Japan when Ohgihara exchanged passes with Kiyotake and supplied an inch-perfect cross for Otsuto extinguish Egypt's Olympic dreams as Japan marches on to the last four having yet to concede a goal.