Soccer’s world governing body FIFA bans any unsanctioned political, religious or commercial messages on shirts.
The T-shirt was also waved by midfielder Hasan Al-Haydos after he scored to put the Qataris 1-0 ahead in the 25th minute.
The show of support comes at a time when several Arab countries have broken off diplomatic ties with the Gulf state.
Qatar’s Uruguayan coach Jorge Fossati defended his players and then condemned the “ridiculous situation” of the “blockade” on the emirate.
“I don’t see something that can receive a punishment as it is a T-shirt with a picture of the emir,” he said. “It doesn’t say anything against anybody.”
Fossati resigned a few hours after leading his team to a 3-2 win over South Korea, a result that kept the nation’s faint hopes of reaching next year’s World Cup finals in Russia alive.
If Qatar fails in its bid it will be the first World Cup host nation not to have previously qualified for an edition of soccer’s largest tournament.
Qatar has used its oil and gas wealth to recruit players from around the world, with about half of the squad naturalized citizens.