The IAAF issued a statement after the Botswana team claimed the 30-year-old Makwala was fit and healthy and should not have been turned away.
The International Association of Athletics Federations (IAAF) issued a statement after the Botswana team claimed the 30-year-old Makwala was fit and healthy and should not have been turned away from the warm-up track ahead of the final.
However, the IAAF insisted that he needed to be placed in quarantine for 48 hours -- ending on Wednesday -- as he was infected with the highly contagious norovirus.
Public Health England revealed that 30 athletes and support staff had been affected with two cases confirmed as being the norovirus bug at a hotel hosting athletes.
"Isaac Makwala has been withdrawn by the IAAF Medical Delegate from tonight's 400m final after the athlete was diagnosed with an infectious disease on Monday," read the IAAF statement.
"As per UK health regulations, it was requested that he be quarantined in his room for 48 hours, a period which ends at 14:00hrs (1300GMT) tomorrow (Aug 9)."
"These procedures are recommended by Public Health England."
The IAAF said that contrary to what had been claimed by the Botswana team, it had made it clear that under no circumstances could Makwala take part.
"It was clearly explained to the teams in writing on Sunday and in person to the Botswanan delegation, a member of which was present with many other representatives of teams at a meeting that took place at the Guoman Tower Hotel on Sunday."
"The decision to withdraw him from the 200m heats last night and the 400m final today was made on the basis of a medical examination conducted in the warm-up medical centre by a qualified doctor on Monday (Aug 7) and recorded in the electronic medical record system of the championships."
"A copy of this medical record was given to a member of the Botswana team medical staff following the examination."
Makwala had insisted on Tuesday he was ready to run the 400m before the IAAF stepped in. He was then caught on camera being turned away from the warm-up track.
That sparked an angry reaction from the team.
"Isaac has been denied entry to the stadium and has been taken back to the hotel where the team stays," Botswana national sports commission chief executive Falcon Sedimo told the BBC.
"We don't have any official communication from the IAAF pointing to the reasons that have led to Makwala being debarred from competing in the 400 metres final for men."
"I met Makwala this morning before 11am and I also met him again this afternoon at around 1500 hours and the indications were that he was ready and raring to go."
Norovirus is often caught through close contact with someone carrying the virus or by touching contaminated surfaces or objects.
Norovirus, which brings on diarrhoea and vomiting, is rarely serious, with most people making a full recovery within one or two days, without treatment.
However, Shirley Kirnon, Senior Lecturer in Infection Prevention and Control at the School of Health Sciences at Birmingham City University, warned that organisers faced a race against time to prevent it spreading like wildfire.
"The main issue facing the organisers will be one of trying to attain swift containment, which will be pretty challenging due to the nature of the virus," she said.
"It is highly infectious and with vast numbers of people -- athletes, site personnel and visitors –- in such close proximity, exposure to affected individuals cannot be contained easily."
Kirnon added that it was crucial those affected were kept away from presently healthy individuals.
"In terms of public health, the emphasis should be to limit the exposure to others," she said.
"This involves limiting social integration and movements of affected individuals."
"For athletes (that means) staying in the rooms whilst having active symptoms (or) remaining within the designated camp, and (for) visitors with symptoms (it means) staying away from public areas."