Just four months ago and only a few miles across south London, Federer was celebrating his record eighth Wimbledon title after crushing Cilic in a brutally one-sided final.
Cilic had been hampered by a blistered foot and the Croat was reduced to tears during the match as his predicament sunk in.
In their first meeting since that All England Club showdown, Federer haunted Cilic once again as he fought back at the O2 Arena.
Having beaten Jack Sock and Alexander Zverev in his first two matches, Federer was already guaranteed to qualify as the winner of the Boris Becker group, but he didn't take it easy against Cilic.
By extending his current winning streak to 13 matches, the 36-year-old advanced from the Tour Finals group stage with an unblemished 3-0 record for the 10th time in his glittering career.
With Andy Murray, Novak Djokovic and Stan Wawrinka all absent due to injury and world number one Rafael Nadal withdrawing after his first match due to a knee problem, Federer appears to have a clear path to his seventh triumph in the season-ending event.
"It was a tough match. I was in trouble, a set and a break point down, but I found a way out of it and I'm happy to be playing this way," Federer said.
"It's nice to play tennis this freely. It gives me a great idea how I want to be on Saturday. I'm looking forward to facing (David) Goffin or (Dominic) Thiem."
The prize money from Federer's win over Zverev on Tuesday took him past golfer Tiger Woods to become the world's highest earning athlete, with a career total of £84 million ($110 million, 94 million euros) according to Forbes.
But Federer is motivated by his legacy rather than the size of his bank balance and winning the Tour Finals for the first time since 2011 would be another feather in his cap at the end of a remarkable renaissance year.
When Federer missed last year's Tour Finals through injury, it seemed possible he would never recapture his former glories.
But this year Federer has been revitalised, winning the Australian Open and Wimbledon among seven titles -- more than other male player over the last 11 months.
Cilic was already eliminated after two successive defeats and could have been forgiven for wanting to get the match over with as quickly as possible before heading off for his holidays.
But the 29-year-old was the more aggressive player in a tight first set which he eventually won in a tie-break.
Federer kept plugging away and the world number two was rewarded when Cilic made a couple of costly errors at 4-5 to surrender the second set.
That was Federer's first break of serve in the match and he quickly added a second, unloading a thumping winner down the line to take a 2-0 lead in the final set.
That was all the advantage Federer needed as he looks ahead to Saturday's semi-finals.
Later on Thursday, German third seed Zverev and American eight seed Sock will stage a winner-takes-all clash as they fight for a semi-final berth.
Both Zverev and Sock have one win from their two matches and the victor will finish as group runner-up behind Federer.
Grigor Dimitrov has qualified from Pete Sampras group and will be joined in the last four by the winner of Goffin's clash with Thiem on Friday.