A Federer serve which appeared to have just landed outside the line towards the end of a back-and-forth first game of the opening set was ruled as an ace, with Del Potro's subsequent challenge request declined due to a problem with the replay technology.
A fuming Argentine became easy pickings for Federer, who utilised a deft array of drop-shots and well-placed forehands to outclass the number nine seed, racking up 13 aces without reply in the process.
"There was a problem with that call," Del Potro said. "It was clear out and the machine doesn't work. The chair umpire told me he made a mistake.
"After that, I was not concentrating in the match and Roger was playing better, taking all his opportunities. I don't feel comfortable playing the match, but that was my problem. Roger made his job, and he's a good winner."
In a statement, the ATP Tour said: "If Hawk-Eye does not have data, as per ATP rules, the original call stands. We understand there was a loss of an internet connection and the data could not be provided."
Federer also felt his first serve had landed wide.
"I thought the ball was out, and that was it, basically," the 30-year-old Swiss said. "And then you just go with the call of the umpire and you sort of move on with it.
"You have these bad calls from time to time. You move on.
"There's a good call, bad call, the worst that can happen is you run out of challenges and the umpire then misses everything and the linespeople too."
An 11-minute opening game, stuck at deuce for some time with both competitors failing to convert two advantage points each, appeared to hint early at a tight and closely-fought affair, until the technological glitch leading to Federer's third allowed the Swiss to eventually hold his serve.
The situation clearly rattled Del Potro, who argued the toss for several minutes with the apologetic umpire before succumbing his serve and going two games behind.
Though his serve recovered throughout the remainder of the set, Federer himself remained strong with the ball in hand to remain ahead until he clinched a 1-0 lead in game nine, ironically after successfully challenging an out call at 30-15.
The unrelenting game of the number three seed picked up where it let off from the onset of the second set, breaking Del Potro's serve in game one before the double-break made it 4-1, a comeback looking all-but-impossible from the submissive Argentine.
Though Del Potro's strength in serve made a cameo re-appearance to take game seven, Federer had room to absorb a hit before wrapping up the comprehensive victory from deuce in the eighth.
"This was for me a really good match against a great player," 16-times Grand Slam champion Federer said after beating Del Potro for the fourth time this season.
"I'm happy I was happy to maintain the great streak I've got going against him this year. He's a top-10 player, a very dangerous player.
"I sort of expected myself to come out and play a good match today after the struggle I had against (Thomaz) Bellucci," said the Swiss, referring to his 3-6 6-3 6-4 win over the Brazilian in the previous round.