Agnieszka Radwanska, the women's top seed in Sydney, set up a semi-final against China's Li Na after both won their quarter-finals in much cooler conditions than the 40 degrees Celsius heat which threatened to suffocate the players on Tuesday.
Sydney men's second seed Gilles Simon pulled out before his last 16 match because of a neck injury, while Kei Nishikori and world number nine Janko Tipsarevic became the second and third players to quit the eight-man Kooyong Classic exhibition event.
All are expected to play at Melbourne Park next week.
World number 13 Isner, however, was hampered by a bone bruise to his right leg in his 6-4 6-4 defeat to qualifier Harrison and was left thinking about pulling out of the year's first grand slam.
"It's better. Definitely better than I thought, but it's not 100 percent," the American told reporters. "I don't know. I've got a decision to make shortly.
"Certainly I could win a match maybe, a match or two. I don't see myself winning the whole tournament at this point, that's for sure."
Australian Bernard Tomic confirmed his return to form by riding his improved serve to a 7-6 6-2 win over fifth seed Florian Mayer and setting up a quarter-final against defending champion Jarkko Nieminen.
"He's one player I don't like playing," Tomic said of German Mayer. "He's a great player, he beats the top four when he's playing well... I'm playing really good tennis."
"The week before the slams, players don't want to take any risks, which is normal but sad also for this one because Sydney is a very nice tournament and deserves to have a very nice draw," 2011 Sydney champion Simon said.
"We just try the maximum to be ready... I mean, for me today, there is no point in me going out and losing 6-2 6-2 playing 50 percent."
Former US Open champion Juan Martin Del Potro knows all about injury setbacks but the Argentine world number seven got his 2013 season underway at Kooyong with a 6-4 3-6 7-6 round robin win over Paul-Henri Mathieu.
Japan's Nishikori, the world number 18, was forced to pull out with a knee injury, while Tipsarevic, a winner in Chennai last week, was a set down to Marco Baghdatis when he retired with a wrist injury.
There was better news on the weather front in Sydney with temperatures of around 25 degrees Celsius at the Olympic Tennis Centre.
ATP Sydney results
3-Andreas Seppi (Italy) beat John Millman (Australia) 6-2 3-6 6-3
Bernard Tomic (Australia) beat 5-Florian Mayer (Germany) 7-6(4) 6-2
Ryan Harrison (US) beat 1-John Isner (US) 6-4 6-4
Jarkko Nieminen (Finland) beat Ivo Klec (Slovakia) 6-3 6-1
Kevin Anderson (South Africa) beat Feliciano Lopez (Spain) 6-3 6-4
Denis Istomin (Uzbekistan) beat 4-Fernando Verdasco (Spain) 6-3 6-3
Julien Benneteau (France) beat 6-Radek Stepanek (Czech Republic) 0-0 (Stepanek retired)
ATP Auckland results
1-David Ferrer (Spain) beat Lu Yen-Hsun (Taiwan) 6-4 2-6 6-3
3-Tommy Haas (Germany) beat Igor Sijsling (Netherlands) 6-3 6-4
Gael Monfils (France) beat Greg Jones (Australia) 6-4 6-2
Jesse Levine (Canada) beat Brian Baker (US) 7-5 6-4
Lukas Lacko (Slovakia) beat 8-Thomaz Bellucci (Brazil) 6-3 7-5