Professor Jiri Dvorak said FIFA's guidelines state that if there is any doubt about concussion then the player should be removed from the field of play.
Dvorak said there was a "99 per cent probability" that Lloris would have been concussed after being knocked out when his head made contact with Romelu Lukaku's knee. The Everton striker needed an ice-pack on his knee afterwards.
Spurs boss Andre Villas-Boas said he made the decision for French goalkeeper Lloris to continue, a move which has been criticised as "dangerous" and "irresponsible" by brain injury charity Headway.
FIFA hosted a conference on concussion in sport a year ago, and earlier this year updated its guidelines, which are followed by the Football Association.
Dvorak told Press Association Sport: "The player should have been substituted. The fact the other player needed ice on his knee means it's obvious the blow was extensive.
"It's a 99 per cent probability that losing consciousness in such an event will result in concussion."
Villas-Boas said Lloris had been determined to continue, but admitted: "He doesn't remember it so he lost consciousness. It was a big knock but he looked composed and ready to continue."
Dvorak added that the player's view should not be taken into account in such situations.
He said: "When he has been knocked unconscious, the player himself may not see the reality.
"I do not know the details but I know that the Premier League doctors are extremely good and I can imagine that the doctor may have recommended he be replaced.
"We have a slogan: if there is any doubt, keep the player out."
Dvorak said any player suffering concussion needed to rest for at least a week - some advice states three weeks - and subjected to further tests.
FIFA's concussion guidelines, also agreed with the international rugby union, ice hockey and equestrian federations, state: "With every impact to the head, it is important that you always think of concussion and watch out for it. If you feel a little out of sorts, but think you can still play, that may not be a good idea. The safest is: "when in doubt, keep out"."
The Tottenham manager praised the goalkeeper's "great character" for wanting to continue, and cited a good late save as evidence that he was correct to do so.
But Headway believes Lloris should have been withdrawn immediately.
Luke Griggs, spokesperson for Headway, said: "We are hugely concerned that a professional football club should take such an irresponsible and cavalier attitude to a player's health.
"Guidelines from both Headway and the National Institute for Health and Care Excellence (NICE) state people should not play any contact sport for at least three weeks after suffering a concussion."
Problems with concussion are not commonplace in football, but rugby players from both codes have to deal with significant blows to the head on a regular basis.
The problem became so worrying for Dr Barry O'Driscoll, uncle of Ireland player Brian O'Driscoll, that he resigned from his role as medical advisor to the International Rugby Board in protest at the decision to trial a new protocol for dealing with head injuries.
The Rugby Football Union is so concerned about concussion that it is holding a conference at Twickenham this week with players' unions on the matter.
The FA has detailed regulations on head injuries and concussions and though it is understood the governing body is not investigating the club's handling of the incident, the rules state that anyone suffering unconsciousness should not play again that day.
The FA regulations state: "Any player remaining immobile and unresponsive to verbal commands following a head injury will be regarded as being unconscious and treated in accordance with established principles for extrication and management of the unconscious player. There will be no return to play during that day."
The rules do however allow for "a transient alteration of conscious level" following a head injury, which says a player can return to play following assessment by medical staff.
"The player will only be allowed to resume play if asymptomatic and with normal co-ordination. The medical attendant should alert the coaching staff, and the player closely observed for any deterioration in playing ability," the regulations say.