Tries by Pieter Labuschagne, Michael Leitch, Kazuki Himeno and 13 points from the boot of Rikiya Matsuda gave Japan a comprehensive victory as they leapfrogged their opponents into second place in Pool D with nine points.
Samoa, who had Ben Lam red carded early in the second half and answered with tries by Seilala Lam, Duncan Paia'aua and Christian Leali'ifano as well as points from the tee by Alai D'Angelo Leuila and Leali'ifano, are third on six points.
With 14 points, England cannot finish outside the top two. Fourth-placed Argentina are expected to add to their four points when they meet Chile on Saturday before a potential pool decider against Japan in the last round of group games.
Both nations went into this game in Toulouse with a realistic chance of qualifying from Pool D - but only if they won.
Japan, seeking a second successive last-eight place, started the stronger and scored from their first major attack on 13 minutes.
Lomano Lemeki drove into space, bouncing off two Samoan defenders before being held up five metres out. The ball came to Labuschagne who bundled over.
Following an exchange of penalties, Japan appeared to take control of the match as they scored their second try and Samoa had a man sin-binned within a matter of seconds.
Jonathan Taumateine was yellow-carded for a tackle off the ball in the build-up to Leitch extending Japan's lead, as they shifted the ball out to the left again and were too quick for Samoa.
This sprang Samoa - who have not reached the knockout stage in 28 years - into life.
After the game was made 14-men apiece when Japan hooker Shota Horie was sin-binned, Samoa's own number two Seilala Lam touched down following a giant maul.
But the Pacific Islanders were their own worst enemies. In the opening minutes of the second period, Ben Lam was given a yellow card for an upright tackle and nasty clash of heads - which was later upgraded - before Kazuki Himeno scored following a Japan maul.
Samoa gave themselves hope and a losing bonus point through Duncan Paia'aua and Christian Leali'ifano tries, but Japan held out via Matsuda's reliable boot.
Japan, who are aiming to repeat their performance as hosts four years ago when they reached the knockouts, face what looks likely to be a winner-takes-all meeting with Argentina on 8 October.