But the Scottish Football Association has now released its written reasons explaining why Flanagan's suspension was overturned.
The former Liverpool defender was booked by referee Kevin Clancy after knocking Hoops skipper Brown to the floor as they jostled at a corner during Rangers' 2-0 derby triumph at Ibrox.
However, Scottish Football Association compliance officer Clare Whyte decided a yellow card was not enough and opted to issue Flanagan with a two-game ban after consulting with three former match officials.
All three agreed the 26-year-old should have been dismissed, with one even claiming he had used his arm and elbow "as a weapon" during the flashpoint.
But that view was dismissed by the SFA's fast-track tribunal which met at Hampden on May 17 to decide Flanagan's fate.
Under SFA rules, an offence witnessed by a referee can only be retrospectively punished as long as the incident ticks off at least one of the following criteria - the involvement of excessive force, brutality or a resulting serious injury.
However, Whyte told the panel she would only be arguing for Flanagan to be punished on the basis the clash featured brutality, which she defined as "savage, ruthless or deliberately violent".
But after hearing Whyte, Flanagan and Rangers' lawyers all present their cases - which included both sides offering video replays of the incident - the panel backed Flanagan.
It rejected Whyte's claims that the Rangers man had struck Brown in the face, insisting Flanagan had "made contact with the chest/neck area of the opponent".
Flanagan told the panel he was "merely fending off" the Celtic captain as he "stood his ground, following initial contact with the opponent, as they awaited the corner kick".
In conclusion, the panel said: "Having viewed the available footage of the incident, provided by both parties, and having considered the submissions from both parties, the Fast Track Tribunal decided that the notice of complaint should be dismissed.
"The referee saw the incident in question, and, notwithstanding that he did not see the actual point of contact, he saw sufficient to assess brutality and decided that the action of the player was reckless.
"The Fast Track Tribunal took the view that the player made contact with the chest/neck area of the opponent, not with his face or head, and that the evidence did not meet the 'exceptional' test in Judicial Panel Protocol 3.3. Accordingly, the Fast Track Tribunal dismissed the complaint."
Responding to the ruling, an Ibrox spokesman said at the time: "Obviously we have concerns about the process but we are happy that the correct decision has been upheld."
The Light Blues had earlier criticised the SFA for getting involved after referee Clancy had dealt with the matter on the field.
They also questioned why Hoops defender Jozo Simunovic was not also issued with a notice of complaint following an off-the-ball collision with Jermain Defoe.
It is understood that the compliance officer also referred the Simunovic incident to the three former match officials but there was no unanimous agreement that he should have been sent off.