With 12 minutes of the 0-0 draw remaining, Lloris was accidentally caught on the head by the knee of Romelu Lukaku as he dived to collect a stray ball.
The Frenchman required lengthy treatment after the incident, and looked set to be replaced by Brad Friedel, but he insisted he was fit to continue and Villas-Boas decided against making a substitution.
The Tottenham manager's actions have been condemned by brain injury charity Headway.
"We are hugely concerned that a professional football club should take such an irresponsible and cavalier attitude to a player's health," said Luke Griggs, spokesman for Headway.
"When a player - or any individual - suffers a blow to the head that is severe enough for them to lose consciousness, it is vital they urgently seek appropriate medical attention.
"A physio or doctor treating a player on pitch simply cannot accurately gauge the severity of the damage caused to the player's brain in such a setting as there may be delayed presentation of symptoms.
"By continuing to play, the player may have caused greater damage to his brain. He should have been removed from the game immediately and taken to hospital for thorough tests and observation."
Villas-Boas conceded after the game that Lloris could not remember a single thing about the incident.
But the Portuguese defended the decision to keep the player on the pitch, citing a good late save from Gerard Deulofeu as evidence that he was correct to do so.
The Tottenham manager praised the goalkeeper's "great character" for wanting to continue, but Headway believes Lloris should have been withdrawn immediately and rested for three weeks.
"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," Griggs said.
"Sports science has evolved significantly over the past decade and yet we're still faced with the antiquated concept that a player should be brave and try to continue at all costs.
"Mr Villas-Boas' comment that his player's determination to play on was proof of his 'great character and personality' is simply wrong and dangerous.
"You are not a hero if you play on after suffering a concussion; all you are doing is risking your health. Football has to react to this and bring in stricter measures to ensure no similar risks are taken in the future."
Source: PA
Source: PA