The world number two continued his unbeaten run into the new season with a 4-3, 2-3, 3-4, 4-0, 4-3 win over the Australian in the short-form contest.
Coming off a four-match winning run in Brisbane, where he took the title in three sets over Milos Raonic on Sunday, Federer started where he left off.
The match featured an experimental style of play, with sets being won after four games, no deuces and play allowed to continue after lets on serve.
The shorter breaks between the changes of ends certainly worked, speeding up the pace considerably.
The format has been piloted at clubs across Australia and is being billed as the Twenty20 of tennis, a reference to the fast and furious form of cricket that has proved a huge hit.
Great friends off the court, Federer and Hewitt have one of the most enduring rivalries in tennis.
The pair, both aged 33, have faced each other 27 times since 1999, with Federer winning 18 of them.
Federer was pushed all the way by his evergreen rival, the contest going its full allotment of five shortened sets.
Both players looked in good touch. On plenty of occasions in the first set and a half Hewitt told Federer his shots were "too good" before the world number 86 found some rhythm to get back into the contest.
Hewitt, who lost in the opening match of the Brisbane International against compatriot Sam Groth in his only other hit-out of the year so far, will now head to his home town of Adelaide to play an exhibition match against Czech Tomas Berdych.
This will round out his formal preparations for the Australian Open.
Federer is expected to head straight to Melbourne for the year's opening grand slam.