The 6ft 6in Argentinian offered the self-deprecating quip following his 7-6 (7/3) 4-6 6-3 victory against the two-time defending champion at London's O2 Arena.
Federer had already qualified and will meet Andy Murray in the semi-finals on Sunday evening, with Del Potro taking on world number one Novak Djokovic in the afternoon.
Bizarrely, the match-ups were not decided until the final round-robin match this evening between David Ferrer and Janko Tipsarevic, even though neither could qualify themselves.
In the end, Ferrer's 4-6 6-3 6-1 victory meant he joined Federer and Del Potro on two wins in Group B but his record was the worst in terms of sets won and lost, with Federer top by that criteria.
Federer had beaten Del Potro in 13 of their previous 16 meetings but the Argentinian has often given him problems, particularly this year in tight matches at the French Open and the Olympics.
And Del Potro won their most recent match in the final of Federer's home-town tournament in Basle two weeks ago, making it back-to-back indoor titles after also winning in Vienna.
The 24-year-old is back at the O2 for the first time since reaching the final in 2009 having battled his way back from a serious wrist injury, but he was reluctant to talk up his chances of a repeat.
Del Potro said: "Beating Federer is not easy for sure. But I didn't think about trying to qualify for the next round.
"I was just thinking about my match and doing the same things like Basle. At the end I was thinking maybe it could be my last service game of the year.
"So I put all my concentration into serving and that helped me to make fantastic first serves and many aces.
"But he's still the favourite to win the tournament, with Murray and Djokovic. Now you have three big names in the semi-finals and one big guy.
"I'm the number four for sure. But everything can happen. I beat Federer, Novak and Andy a long time ago, so maybe if I am lucky I can repeat that here."
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In a tight first set it was Federer who had the only chances to break, three of them in the eighth game that he could not take, and a poor tie-break from the world number two put him behind.
He hit back straight away by winning the first eight points of the second set but was broken at the start of the decider and won only two points against the Del Potro serve in the final set.
"It's disappointing," said Federer. "I had a good feeling going into the match, definitely the right game plan. It's indoor tennis, he has a big serve and all those things. But still I expect myself to get more returns into play.
"But it's important to move on right now. Mentally, it's important to look ahead and rest because it's a quick turnaround. I tried everything I could and was a bit frustrated at times, but it shouldn't affect me tomorrow."
Federer does not believe playing two days in a row will be a disadvantage for him or Del Potro but admits that the schedule become a factor if either makes it through to Monday's final.
The 31-year-old, meanwhile, revealed a major source of disappointment was that his defeat eliminated world number five Ferrer from the competition before his final match.
The Spaniard has been one of the players of the season, winning seven titles, the best on the ATP World Tour, and reaching the semi-finals at the French Open and US Open.
Federer added: "I was thinking more about David than I was thinking about Andy and Novak, to be honest. I really wanted to give him a chance. I'm more disappointed for him than I am about losing today [Saturday]."
Ferrer will head to Prague ahead of next weekend's Davis Cup final between the Czech Republic and Spain, but he felt a little hard done by in the manner of his exit.
The 30-year-old said: "I think maybe we could have played first. I talked yesterday [Friday] with the ATP and I expressed my opinion.
"It was not easy because I knew before the match if I won I would not qualify for the semi-finals. I began very bad but in the second set I played better. It was important because I have 200 more points and it's good for next year."