An FFA statement said: "The MRP (Match Review Panel) determined that Lowe committed the offence of Use of offensive, insulting or abusive language and/or gestures towards a match official. The MRP has proposed a sanction of two matches, being the Mandatory Match Suspension plus one (1) additional match."
Lowe can appeal the second match ban but must serve a mandatory one-game ban.
In a post-match interview with SBS, Lowe claimed he had "selective amnesia" when asked about the incident.
Lowe was incensed after City's Bruno Fornaroli had been awarded a controversial penalty late in the first half.
Perth went on to win the match 3-2 thanks to a hat-trick from striker Andy Keogh.
Glory face Brisbane Roar away and Western Sydney at home in their next two matches.