Muresan was also fined 25,000 lei ($7,100) following the ugly incident in the game against champions Steaua Bucharest on Oct.
26, the FRF added in its statement on Wednesday.
Referee Istvan Kovacs came under fire after showing Muresan a yellow card after he knocked Steaua striker Raul Rusescu down with an elbow, with the Romania international undergoing surgery following a zygomatic bone fracture.
Doctors said Rusescu, who will be out of action until the New Year, was close to losing his eye.
Local media described Kovacs’s performance as shameful after Steaua coach Constantin Galca had to make three substitutions in the first 28 minutes with strikers Rusescu and Claudiu Keseru and defender Iasmin Latovlevici all injured by fouls.
Another Targu Mures player, Ousmane N’Doye, got a six-match ban after Keseru suffered concussion following a reckless challenge by the Senegalese midfielder. N’Doye was shown a red card after the game for a skirmish in the centre of the field.
Keseru was taken to hospital and hours after the match said he could not remember when and why he had been substituted.
Targu Mures won 1-0 to inflict Steaua’s first away defeat in the league since their 3-1 loss at Brasov on Nov. 26, 2012.
“It’s a drastic decision, I’ve never seen anything like this,” Targu Mures’s general director Daniel Stanciu told local media. “How a player can be suspended for 16 matches since he wasn’t even sent off?”
“And I don’t understand N’Doye’s ban too. We’ll appeal.”
Steaua, the 1986 European Cup winners and Romania’s most successful club, also accused Kovacs of committing a number of errors, including not awarding them a penalty in the second half and instead wrongly booking Cristian Tanase for diving.
Gazeta Sporturilor, one of the country’s most popular newspapers, gave a referee’s performance mark of zero out of 10 for the first time.
Following the injuries Galca has been forced to include four players from the junior team for their national cup match at Politehnica Iasi.
Steaua top the league standings with 31 points from 13 matches. Targu Mures are fifth on 23.
($1 = 3.5387 Romanian Leus)
(Reporting by Angel Krasimirov; Editing by Ken Ferris)