The Korean brought down Kevin De Bruyne and got a one-game ban, as the Spurs winger will now be forced to sit in the stands.
In one of the most memorable games in Champions League history, Manchester City beat Tottenham 4-3 on the night at the Etihad Stadium.
But the north London side prevailed 4-4 on aggregate thanks to the away goal rule, sealing their place in the last four for the first time in their history.
Son was one of the heroes on an incredible night for Spurs scoring twice in a sensational quarter-final tie but he will not have the chance to play in the first leg following his booking.
That leaves Tottenham coach Mauricio Pochettino with a selection dilemma with star striker Harry Kane ruled out for the rest of the season with an ankle injury.
It could see Spanish target man Fernando Llorente, who scored the clinching goal after coming off the bench, start up front alongside Dele Alli and Lucas Moura for the first leg at the New Tottenham Stadium on April 30.
With Moussa Sissoko coming off injured, however, Pochettino has been left short in central midfield and will be hoping the Frenchman recovers in time for the semi-final.