The club responded to criticism by FIFA's medical chief of the decision not to substitute the French goalkeeper despite him being knocked unconscious by saying medical staff were "totally satisfied that he was fit to continue playing".
Lloris did have a CT scan however after the match in Liverpool and was given the all-clear.
Tottenham said in a statement: "The club can confirm that Hugo Lloris underwent a precautionary CT scan and was given the all-clear and travelled back to London last night.
"The France goalkeeper suffered a knock to the head following a collision with Everton forward Romelu Lukaku in the closing stages of yesterday's Premier League encounter at Goodison Park and was cleared to resume playing after examination by the club's medical team."
Spurs head of medical services Wayne Diesel added: "Once the relevant tests and assessments were carried out we were totally satisfied that he was fit to continue playing."
Spurs boss Andre Villas-Boas confirmed that Lloris had been unconscious and could not remember a thing about the incident but said he made the decision for the goalkeeper to continue.
FIFA's chief medical officer Professor Jiri Dvorak said however 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 Lukaku's knee - and the Everton striker needed an ice-pack on his knee afterwards.
FIFA hosted a conference on concussion in sport a year ago, and earlier this year updated its guidelines.
Dvorak said: "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 because 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.
Villas-Boas' decision has been criticised as "dangerous" and "irresponsible" by brain injury charity Headway.
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."
The Football Association has detailed regulations on head injuries and concussion and though it is understood the governing body is not investigating Tottenham's handling of the incident, the rules state that anyone suffering a loss of consciousness 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 international players' union FIFPro has also criticised Tottenham for allowing Lloris to continue.
FIFPro medical advisor Vincent Gouttebarge said: "FIFPro condemns that the health and safety of players are left to coaches/trainers or even to players themselves.
"Medical professionals should be aware of any relevant medical guidelines and apply them in order to empower the health and safety on the field. The health and safety of the players should be the number one priority and should prevail against any other matters."