Isner was also involved in the longest match when the American beat France's Nicolas Mahut 70-68 in the final set of their first-round match in 2010.
From next year's Wimbledon onwards, a tie-break will be played if the deciding set reaches a score of 12-12.
Wimbledon is the second grand slam to introduce final-set tie-breaks, with singles matches at the US Open decided by a tie-break at 6-6.
At the Australian Open and the French Open, players still have to win by two games in the final set in singles matches.
It always seemed unlikely that we would see another Wimbledon marathon to match the 11hr 5min John Isner-Nicolas Mahut epic of 2010.
It comes after the final set of Kevin Anderson's semi-final with John Isner this year lasted nearly three hours.
The All-England Lawn Tennis Club announced on Friday that it's introducing a new rule to specifically prevent those exhausting, overlong final sets from happening.
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According to Wimbledon CEO Richard Lewis, many players were in favor of the change.
This year, eventual finalist Kevin Anderson played a pair of long matches late in the tournament.
"In reaching this decision, the AELTC Committee sought the feedback of both players and officials, analysed two decades of match data, and considered other factors including scheduling complexities and spectator experience", chairman Philip Brook said.
Both Anderson, 32, and Isner, 33, called on Wimbledon to move to a final-set tiebreak after their marathon match in July's semifinal.
"They recognise it affects the quality of matches in subsequent rounds".
Instead of the final set continuing to go back and forth, with scores that can go into the 40s or 50s, they're cutting it off at 12-12 and introducing a tiebreaker that would end the set and decide the victor.
Other notable long matches include Federer's victory over Andy Roddick in the 2009 final, winning 16-14 in the fifth set.