Ledecky withdrew from the morning's 200m free heats in Gwangju and was assessed by doctors before deciding to also skip the 1,500m final later on Tuesday -- an event she has crushed at the last three world championships.
Sun, who retained his 400m title at the weekend and is favourite to add the 200m title in Tuesday's late final, clocked a pedestrian seven minutes, 48.12 seconds -- but his attempt to conserve energy almost backfired as he squeezed through in eighth spot for the 800m final.
"I went to bed at two this morning and got up at 7:40," said the 10-time world-title winner, who has become embroiled in another simmering feud with Australian rival Mack Horton
"It was my fifth swim this week while most of the others were having their first race. But I don't want to give up any of the events, whether 200 or 800. I'll try to cope."
Horton, warned by swimming's governing body FINA for refusing to join Sun for a podium photo-call after the 400m medals ceremony, failed to qualify for Wednesday's final.
The Aussie branded Sun as a "drug cheat" before beating him to 400m gold at the 2016 Rio Olympics over a prior three-month suspension China's sporting hero served for using a banned stimulant, which he blamed on medicine for a heart condition.
Horton's protest, which comes after a leaked FINA doping report claimed triple Olympic Sun destroyed vials of blood after being visited by testers last September, has sparked a fresh war of words.
- 'Literally training' for Peaty -
Ledecky, who lost her 400m title to Aussie teen Ariarne Titmus in a stunning upset on day one, has complained of feeling unwell since arriving in South Korea, Team USA officials said Tuesday.
But they told AFP that the 14-time world champion had not withdrawn from the remainder of the meet, meaning she could still defend her 800m freestyle title this weekend.
Canada's Commonwealth champion Taylor Ruck and Australian Emma McKeown, who took silver at the 2017 world championships, also pulled out to manage their heavy schedules.
In their absence, Sweden's Olympic silver medallist Sarah Sjostrom topped heat times in 1:55.14 with Titmus third fastest in 1:56.34 and defending champion Federica Pellegrini fifth in 1:56.81.
Adam Peaty, who completed a hat-trick of world titles in the 100m breaststroke on Monday, topped the heat times in the 50m, touching in 26.28 seconds as he chases a golden treble over the one-lap race.
"It was literally training for me," said the Briton.
"I wasn't coming in here this morning with any emotion or any expectation. I'll just let the stroke flow. I've just got to mash up with a technique and mash up with the nerves and emotion and I'm sure it will be a good one."
Hungary's Kristof Milak, tipped for a breakout meet this week, topped the heat times in the men's 200m fly with a time of 1:54.19.