UEFA says its disciplinary panel will judge a single charge relating to field invasions, on Dec. 11.
Play was stopped for 10 minutes when the referee took Tottenham and Partizan players off the field after the third invasion in the first half of Thursday's match.
All three spectators wore T-shirts promoting a company which makes official Tottenham merchandise.
Tottenham apologized to fans for the "totally unacceptable behaviour," and said all three were arrested.
The London club won 1-0 and advanced to the round-of-32.