Makwala was withdrawn from the 400-meter final by the IAAF about five hours before the race, but he had earlier posted on his Facebook page that he was feeling fine.
"It is with a bleeding heart that I formally announce that I will not be part of the 400m final," Makwala later wrote on Facebook. "I arrived at the stadium today ready to run but I found a trap set there ... and denied entrance (Government order by the way not IAAF).
"I still maintain I am not sick and have never been tested by any Doctor. I shall rise again."
The runner from Botswana entered the championships as the main competition for Wayde van Niekerk in both the 200 and 400. On Monday, he pulled out of the 200 heats because of the virus but had hoped to run in the 400 final on Tuesday.
The IAAF said in a statement that Makwala was withdrawn because he was "diagnosed with an infectious disease" on Monday.
"As per UK health regulations, it was requested that he be quarantined in his room for 48 hours," the IAAF said, noting that period ends at 2 p.m. Wednesday. "These procedures are recommended by Public Health England and were clearly explained to the teams in writing."
Last month, Makwala became the first man to run 200 meters under 20 seconds and 400 under 44 seconds on the same day at a meet in Madrid. He also has the top time over 200 this season (19.77 seconds) and has the third-best mark in the 400.
Earlier Tuesday, the IAAF said Makwala was out of the final "due to a medical condition on the instruction of the IAAF Medical Delegate." It is based on a rule which says that the IAAF doctor "shall have ultimate authority on all medical matters."
The virus hit about 30 athletes and staff. Nine people were still being affected, according to the IAAF.
"The IAAF is very sorry that the hard work and talent of Isaac Makwala won\'t be on display tonight," the IAAF said, "but we have to think of the welfare of all athletes."