Stand-in India captain Kohli failed to deal with a first-up short delivery from Johnson on Thursday at the Adelaide Oval, the ball striking him on the helmet as he looked to duck out of the way.
Such an event would usually draw an encouraging response from the crowd and players alike, however concern washed over those in attendance as memories of Phillip Hughes' death came to the fore.
Lyon - alongside national team-mates David Warner, Shane Watson and Brad Haddin - played in the Sheffield Shield match that saw a Sean Abbott delivery fatally injure Hughes.
Kohli recovered to make an impressive 115 before top-edging another steep Johnson delivery to deep fine leg and, after seeing the left-armer return to somewhere approaching his snarling best at the end of the third day's play, Lyon has backed the paceman to fire when the action resumes on Friday.
"Your heart skips a beat," Lyon said of the hit.
"Especially for the four guys out there, I know I went to everyone just to ask if they were okay because it's something that you don't want to see again, when we were out there with Phil's incident.
"And today that sound was pretty familiar.
"That is why we all ran in there quite quickly just to see if he was okay, that is the main thing.
"It's something that you don't want to see ever again, what we saw with Phil.
"It probably has been a positive thing as well, as bad as that sounds - we know the helmets work and to have that confidence for our quicks to bowl the bouncer again.
"I know we spoke about it at lunchtime with Mitch. He is feeling good and I can guarantee he's going to come out and fire in the second innings and have that aggression that we all love him for."