The 26-year-old headed home from a corner to open the scoring, rising highest to meet Granit Xhaka's delivery before using his hands to perform the political gesture.
The Swiss duo could have faced match bans, but instead both were fined £7,600 ($9,850) for making the Albanian eagle hand gesture. Switzerland captain and new Arsenal signing Stephan Lichtsteiner was also fined £3,700 ($4,795) for his part in the goal celebrations at the World Cup.
The International Football Association Board's laws of the game state that players must refrain from "using offensive, insulting or abusive language and/or gestures" or "gesturing in a provocative, derisory or inflammatory way".
Celebrations also should not reference "any local, regional, national or international political party/organisation/group, etc" or "any specific political act/event".
The FA will then decide on punishment and can sanction either the player or team if they decide an offence has been committed.
Mustafi previously spoke about his Albanian background, which saw his grandfather forced to leave the country and move to Germany, speaking about how difficult it is for people to relate to the difficulties of immigration unless they have lived through it.
"You have to understand when people who come into the UK and Germany that you don't know what this person saw in his life before," told the Daily Mail in 2016.
"When I go back to Albania you have six-year-olds who do not go to school and have to work. There are no schools. So they come to this country and it is difficult. We all need to understand the differences. It is complicated but it needs understanding."