The towering Argentine, who won the 2009 U.S. Open, is a dark horse to win his second grand slam title having enjoyed encouraging form in the leadup to Melbourne with victory in the Sydney International warmup event.
The 22-year-old Williams, ranked 130 in the world, had other ideas as he matched Del Potro's firepower in a tense first set and closed it out when the fifth seed stumbled in an error-strewn tiebreak.
Del Potro steadied in the second set and cruised to victory in just over three hours to set up a clash with Spain's 62nd ranked Roberto Bautista Agut.
The extreme heat at Melbourne Park on Tuesday caused a ball-boy and men's player Frank Dancevic to collapse during his first round loss, and the Canadian later slammed organisers as 'inhumane' for not suspending play.
"I tried to focus for the match in the worst conditions to play," Del Potro said in a courtside interview. "Really, really hot but the crowd kept me going.
"Hopefully the weather will be better on Thursday."
Del Potro is unlikely to get his wish, however, with the temperatures forecast to exceed 40 degrees Celsius (108 Fahrenheit) for the next three days until a cool change on the weekend.
(Reporting by Ian Ransom; Editing by Patrick Johnston)
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