The rule was brought in when the 2019-20 top-flight season restarted in June, having been halted for three months because of the coronavirus pandemic.
For next season, the league will revert to three permitted substitutions, after the vote at a meeting on Thursday.
Many members are believed to have felt the five-substitute rule was unfairly benefiting the major clubs.
Fifa had allowed the continued use of five substitutions if leagues wanted.
World football’s governing body said the rule can be used until August 2021, meaning the European Championships and Copa America can adopt it next summer.
“Some competitions which resumed in 2020 may have a shorter-than-usual recovery/preparation period before the start of their next season,” Fifa said recently.
“For many competitions, the 2020-21 season will involve matches being played in a condensed period due to a delayed start and the inability to end later than usual because of major international tournaments.”