The England international being benched means Manuel Akanji starts on the right of a three-man defence
Konta was eliminated early Friday after contesting the latest women's match ever held at the Australian Open, starting at 12:30 am and ending two hours and 42 minutes later at 3:12 am.
An exhausted Konta said the situation should never have arisen.
"I don't agree with athletes having to physically exert themselves in the wee hours of the morning," she told the BBC after the 6-4, 6-7 (3/7), 7-5 second-round defeat to Spaniard Muguruza.
"I don't think it is healthy - in fact it is quite dangerous.
"However, Garbine and I were both in the same position and, with the circumstances, we really put on a great match and it's just a shame more people couldn't enjoy it."
The start was delayed when the men's match between Alexander Zverev and Jeremy Chardy on the same court turned into 3hr 46min epic.
In a bizarre twist, Konta said organisers looked at switching the match to an outside court but found it was covered with bird droppings.
"We were actually going to go out to court three to start. There was basically seagull poo everywhere," she said.
"They had to clean the court. By the time they would have cleaned the court, we would have been in the same boat anyway."
Two-time Grand Slam champion Muguruza was astonished that a smattering of hardy fans stayed in the stands to watch the contest.
"I can't believe there are people watching us at 3:15am," the former world number one said.
"We play for you guys watching, otherwise why are we here? It was very tough."
Muguruza, seeded 18, will meet Timea Bacsinszky of Switzerland in the third round on Saturday.
The previous record for the latest start was set last year when a second-round match between Daria Gavrilova and Elise Mertens began at 11:59 pm.
The latest end to a match at any Grand Slam was also at Melbourne Park in 2008, when Lleyton Hewitt and Marcos Baghdatis finished a five-setter at 4:34 am.
The schedule is largely determined by local television demands to play high-profile matches in the evening prime time.
World number one Novak Djokovic, whose match against Jo-Wilfried Tsonga also ended in the early hours of Friday, had little sympathy for the women's plight.
"It happened many times in the men's (draw), women's as well, that you go after midnight," he said.
"You get to this kind of particular situation where you wait for hours and hours and hours, then you are about to make the decision whether you want to go out on the court or not."
Roger Federer voiced similar sentiments, saying there wasn't much you could do about it.
"Is it ideal? No, it's not. But sometimes what can you do if you schedule a match, especially a men's match before, and that thing goes, you know, four, five hours, and it can happen," he said.
"I mean, you could move them on an outside-court, but then the atmosphere might be quite sad, you know.
"So I think it is what it is. You just deal with it. You move on."
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