Following the 1-0 win in Saint Petersburg, Manchester United midfielder Pogba tweeted: "This victory goes to the heroes of the day, well done boys, you are so strong."
FIFA boss Gianni Infantino had invited the boys' Wild Boars football team to Sunday's World Cup final last week.
But FIFA said it had been informed "that due to medical reasons, the boys will not be in a position to travel to Moscow".
"FIFA's priority remains the health of everyone involved in the operation and we will look into finding a new opportunity to invite the boys to a FIFA event to share with them a moment of communion and celebration," a spokesman said.
The Thai footballers, aged from 11 to 16, had been stuck deep underground after setting off to explore the cave with their coach after training on June 23.
FIFA also expressed condolences to the family of a Thai Navy SEAL who died after running out of oxygen during the rescue operation on Friday. "Our thoughts are with his family," FIFA said.