City took an early advantage with goals from Phil Foden and Josko Gvardiol putting them in charge in the opening 25 minutes at The Etihad, only for Leeds' Dominic Calvert-Lewin to pull a goal back in the 49th minute.
Goalkeeper Donnarumma asked for medical attention a few minutes later, and Guardiola gathered his team to provide additional instructions.
"It is not the elephant in the room. Why he (Donnarumma) went down it was obvious. It is smart," Farke told reporters after the match.
"It is within the rules, so I can't complain," he said.
"If I like it? If it's within the sense of fair play? If it should be like this? I will keep this to myself. It is up to the authorities to find a solution."
Guardiola's change in tactics did not help City immediately with Lukas Nmecha levelling the game in the 69th minute from a rebound after his penalty was saved by Donnarumma.
But City rallied late in the game and Foden found a winner in the 91st minute, scoring his second goal of the night to help his side get all three points.
"We need to educate our players in football what to do in terms of fair play and sportsmanship," Farke said.
"If we just try to bend the rules and even do a fake injury in order to do an additional team talk, I do not like personally."
City climbed to 25 points in 13 games in the league table, reducing gap to four points with leaders Arsenal. Guardiola's side will next face Fulham in the midweek fixture on Tuesday.