Premier League clubs voted against continuing to allow five substitutes for the 2020/21 season on Thursday.
Following the resumption of the 2019/20 campaign after the coronavirus shutdown, clubs were allowed to name nine substitutes and make five changes during matches to support player welfare.
Some clubs wanted the new regulation carried over but the Premier League confirmed they were voted down at Thursday's annual general meeting, held virtually.
All 20 members also backed changes to the video assistant referee as the system is to fall in line with FIFA protocol.
"At the Premier League's annual general meeting today, shareholders agreed to rules relating to VAR and substitute players for the 2020/21 season," the statement said.
"Shareholders unanimously approved the implementation of VAR, in line with the full FIFA VAR protocol.
"Clubs also agreed to revert back to using up to three substitute players per match, with a maximum of seven substitutes on the bench."
The VAR changes come as FIFA aims to have a unified approach to its implementation.
There was controversy in several Premier League games during the season, with the new protocols agreed upon unanimously.
The changes will see referees use the pitch-side review area more often, with the Premier League now also using VAR to spot goalkeeper encroachment on penalties, while assistant referees have been told to keep their flag down for marginal offside calls until the attacking move has played out.