The exit of Isner, who was promoted to No. 1 seed after Jo-Wilfried Tsonga and Richard Gasquet withdrew, followed two more injury withdrawals: second-seeded and 2011 Sydney champion Giles Simon (neck) and sixth-seeded Radek Stepanek (back).
Isner, who withdrew from the Hopman Cup mixed-team competition in Perth last week with a right knee injury, lasted 71 minutes against the 64th-ranked Harrison.
The Australian Open starts Monday, leaving injured players little time to prepare for the season's first major.
In other matches, third-seeded Andreas Seppi of Italy beat John Millman of Australia 6-2, 3-6, 6-3; Australian Bernard Tomic, who beat No. 1-ranked Novak Djokovic last week at the Hopman Cup, advanced with a 7-6 (4), 6-2 win over fifth-seeded Florian Mayer of Germany; and Denis Istomin of Uzbekistan beat fourth-seeded Fernando Verdasco of Spain 6-3, 6-3.
In the women's draw, top-seeded Agnieszka Radwanska of Poland advanced to the semifinals with a 6-4, 7-5 win over Italy's Roberta Vinci and Dominika Cibulkova of Slovakia beat third-seeded Sara Errani of Italy 6-2, 6-1.
After winning the WTA event in Auckland last week, Radwanska has a seven-match winning streak.
"So far I feel good and I'm very happy that I can play good matches, already seven in a row," she said. "I think this year is the first time that I played two tournaments before (the Australian Open). I never did that before. So far it's good and I'm going to keep going."
In night matches, fourth-seeded Li Na of China beat American qualifier Madison Keys 4-6, 7-6 (2), 6-2 to advance to Thursday's semifinal against Radwanska, and second-seeded Angelique Kerber of Germany came from 3-0 down in the second set to beat two-time Grand Slam champion Svetlana Kuznetsova 6-3, 7-5.
Li said she was surprised by the power and big serve displayed by Keys, who Li predicted would rapidly improve on her ranking of 135.
"If she plays a level like this every match she should be soon, top 20, top 15, top 10," Li said. "I got the information she had a big serve but did not think it would be like it was today."
Li won Sydney in 2011 and was runner-up to Victoria Azarenka last year.
"Maybe it's a lucky area for me," Li said.