While Wallabies coach Joe Schmidt had been alert to the possibility of a lightning break and said they had a "plan", television broadcast showed Lions players on their phones in the change rooms during a 38-minute delay of the eventual 22-12 defeat in Sydney.
Players had been ordered off the field due to lightning striking near Accor Stadium early in the second half, when the Lions were trailing 8-0.
Both sides were given 10 minutes to warm up, with the Wallabies shooting out to a 15-0 lead shortly after play resumed.
Grilled by the critical British press to clarify the procedures surrounding the lightning delay, Farrell disputed any suggestions his players had failed to use the time seriously.
"That's completely utter rubbish. Utter rubbish," Farrell said.
"You don't know until you know, and when you do know, then you have to agree that the warm-up time allocated is going to be acceptable to both teams.
"We agreed on 10 minutes for the warm-up, and through our advice from our experts in that field, we only made the call to come out five minutes before and stay there so that we'd be ready to go."
Farrell's Wallabies counterpart Schmidt said he had wanted his players to remain connected during the delay.
"We had been warned that there might be lightning, so we had a little bit of a plan," Schmidt said.
"We wanted to make sure that players kept moving, so we had different guys rotating on the bikes.
"We had four balls in the change room that we were just throwing around, just so they could stay connected."
The Wallabies emerged the better side following the delay, with Farrell labelling winger Max Jorgensen's stunning 50-metre runaway try in the 55th minute as "the try that broke the camel's back".
"I suppose what came off the back of that is that Australia hit the ground running and thoroughly deserved their win," Farrell said.
"Rigor mortis was setting in at one stage there for the lads.
"Anyway, I suppose that's what you come to expect with a schedule like a Lions schedule, so we've seen it all now, haven't we?"
A serious head knock to Lions lock James Ryan had soured the opening minutes of the second half, just minutes before the lightning delay.
Ryan had to be stretchered off after copping an accidental knee to the head from Will Skelton, but Farrell confirmed the 29-year-old was in "good spirits".
"He's up and talking. He was out there for a good few minutes," Farrell said.
"But he's back up in good spirits, so hopefully he's going to be fine."
Lions lock Tadhg Beirne, named player of the series, could only describe the loss as a "bittersweet moment".
"We lost tonight, which is obviously a bit crap for us," Beirne said.
"But as 'Faz' says, we'll get over that because at the end of the day, we still won the series.
"It's the last time we'll be in that change room together as a group, and I suppose that's the bitter part, that we won't get that moment again."
