The four sides above them - Man Utd, Newcastle, Chelsea and Liverpool - already had places in Europe, so City were next in line.
The Fair Play league looks at whether the players' respect each other and the referee's decisions, as well as the behaviour of the crowd and team officials.
City finished ninth in the Premiership.
The league had the best disciplinary record in Europe, the reward for which was City's cup place.
The draw for the Uefa Cup qualifying round will take place on 20 June.