The incident occurred just after Andros Townsend had given Tottenham a 1-0 lead over Aston Villa in a Premier League game that saw the London club go on to win 2-0.
Bryan was hit on the back of the head by the flare, which was thrown from the section of the ground allocated to Tottenham fans.
An FA spokesman said: "The FA will investigate this matter, which is unacceptable.
"We will await the match officials' report and will be speaking to the clubs.
"Such incidents highlight the dangers of pyrotechnics being used in a football stadium."
"It is not great to see," said the Portuguese.
"It should be avoided completely. It touched the linesman and situations like this don't have a place in football. I sincerely hope it doesn't happen again."
TOPICS
LATEST ARTICLES
