His fellow team-mates Grant Xhaka and Xherdan Shaqiri were also charged by football´s governing body following a celebration following their goals.
The trio made a bird-shape with their hands, alluding to the Albanian flag given the Albanian origin of the two goalscorers. The symbol sparked outrage among Serbians, in a region where tensions between various ethnic groups have been high for decades.
It was revealed that the Swiss full-back joined in with his team-mates' celebration, and with FIFA charging them for the gesture Lichsteiner had to face the same fate.
The Serbian FA are also facing repercussions from FIFA for comments made after the match by their president Slavisa Kokeza and coach Mladen Krstajic, along the same political lines as the motivation for the said celebrations.
The goal-scoring duo will have to pay fines of 10,000 Swiss Francs to FIFA in response to the charges, while Lichsteiner faces a fine of 5,000 Swiss Francs for his role in the celebration.
Switzerland face a crucial final group game against Costa Rica, with a win guaranteeing them a place in the last 16 of the World Cup, as they managed to do at the last tournament in Brazil.