Verstappen overtook Hamilton on the final lap in Abu Dhabi to win the 2021 title after a late safety carFormula 1's safety car rules have been changed to make it impossible for a race to be conducted in the manner of 2021's controversial title decider.
Masi's actions had a direct result on the outcome of the world championship.
Governing body the FIA has now made it clear "all" lapped cars must un-lap themselves before a restart.
The change replaces the phrasing in last year's rules, which said "any" lapped cars between the leaders should overtake and join the back of the field before a restart after a safety car.
Masi's decision to allow only the cars between race leader Lewis Hamilton and title rival Max Verstappen to un-lap before a restart was at the heart of the Abu Dhabi controversy.
It meant not all drivers in the field were treated equally - as lapped cars between Verstappen and third-placed Carlos Sainz's Ferrari, and others further down the field, were left in place.
McLaren's Lando Norris said the climax to the race had been "made for TV" and his team-mate Daniel Ricciardo added: "I'm glad I wasn't part of that."
Hamilton had dominated the race and was on his way to an eighth world title. But after the restart the Mercedes driver was left exposed on old tyres and passed by Verstappen's Red Bull, earning the Dutchman a maiden championship.
Verstappen's Red Bull team used this as an argument that Masi had not erred in his procedures and the result should stand. And the stewards also used it to retro-fit a justification for Masi's actions and keep the outcome in place after Mercedes lodged an appeal after the race.
The second rule at the heart of the Abu Dhabi controversy has been left unchanged.
This is the requirement the race must be restarted "at the end of the following lap" after the message is relayed that lapped cars may now overtake.
Masi ignored this rule and restarted the race at the end of the lap on which he had ordered only some lapped cars to pass the leaders.
Had he followed the rules as intended on this aspect, the race would not have restarted and Hamilton would have been world champion.
The rule changes are the latest in a series of moves by the FIA that amount to an effective admission Masi made mistakes in his handling of the Abu Dhabi race.
The first was the admission that the controversy was "tarnishing the image" of F1 and the decision to launch an inquiry into what had happened.
After conducting the inquiry, Masi was removed as race director and replaced by two two new officials who will alternate in the role, Eduardo Freitas and Niels Wittich.
And the support structure in race control was beefed up, including the establishment of a department similar to football's video assistant referee (VAR) and the return of F1 veteran Herbie Blash in an advisory role to the race directors.
Blash, 73, was the right-hand man of former FIA F1 director Charlie Whiting, whose death on the eve of the 2019 season led to Masi being appointed race director.
A full report into the events of Abu Dhabi is expected to be published during this weekend's season-opening Bahrain Grand Prix.
It is widely accepted within F1 that Masi did not follow the rules correctly.
The closest there has been to an explicit admission of that fact by the FIA has been an interview by executive director of single-seaters Peter Bayer.
He said that, had Mercedes pursued their appeal, it would likely have been decided that "it's different in the regulations, he [Masi] decided that [other] way, so we could just void the result".
Had the race been declared void, Verstappen would still have been champion as he started the event ahead in the championship by virtue of results count back.
