The Scottish Championship leaders lost 3-2 to the Bairns in dramatic fashion.
With the Light Blues 2-0 up, Warburton made all three changes in the space of 10 minutes, taking off both goalscorers, Kenny Miller and Barrie McKay, as well as Billy King, and replacing them with forwards Michael O'Halloran and Nicky Clark and attacking-minded midfielder Harry Forrester.
The choices seemingly proved costly as Peter Houston's side scored three times in the final 18 minutes to seal a stunning win, and Warburton's tactics came in for questioning after taking off both goalscorers who had looked impressive all game.
Despite the way the game panned out following the substitutions however, Johnstone has claimed that the result was not down to the changes that the former Brentford boss made.
"To be fair, it wasn't the forward players that cost Rangers on the night, it was the defence that let them down," he told the Evening Times.
"The first goal, you can't do a lot with it and it is a strike in a million. Blair Alston won't score a goal like that again so you have to put your hand up there.
"But the second and third goals were poor to lose. That wasn't down to the substitutions.
"The reaction has maybe been a bit over the top. Yes, we lost a game we should have won, but these things happen in football."
With an 11 point lead at the top of the table - with the added bonus of a game in hand over Falkirk - Warburton could surely be forgiven for adopting a philosophy of throwing fresh legs on in attack to ensure that their opponents would have been unable to think about getting forward as they would have had enough problems in defence.
While that strategy did not work on that occasion, the cushion at the top allowed for the problem to be highlighted at a time when there should be very little consequence from losing the game.
And if McKay or Miller had sustained an injury during the final half-hour of the game - especially one that could have left their chances of featuring in the Scottish Cup semi-final with Celtic next month in doubt - Warburton would surely be facing questions about deciding not to bring them off when the game looked won.