Is it permissible to have a non-linear narrative in a three act structure?

You wouldn't be breaking any rules because none exist. The rules are a bundle of advice at best, and not all advice is equally useful.

Yes, you can have a non-linear narrative in a three act structure. Take this outline for example:

(1) A man accused of murder appears in court.

(2) He reflects on his relationship with the victim and the events leading up to the murder.

(3) The judge sentences him to 20 years in prison.

Sentence #2 takes place before sentences 1 and 3, yet they all still map to the three acts of setup, conflict and resolution.

The three-act structure controls the flow of dramatic tension: low at the start, high at the climax, then low again at the denouement. If a chronological telling of events would negatively impact that tension, a non-linear narrative could be just the thing you need.