After taking the wicket of opener Murali Vijay before lunch on day three at the Adelaide Oval, a fired-up Johnson banged in a short ball which struck Kohli flush on the badge of his helmet.
With all mindful of fallen batsman Hughes', who died in hospital two days after being hit in the neck by a bouncer, the Australian fielders bolted to the middle out of concern for Kohli, who took his helmet off to inspect it.
Though fans at the ground had applauded the first short ball that India's Varun Aaron sent down to opener David Warner on day one, the Kohli hit hushed the terraces and Australia captain Michael Clarke consoled Johnson as he walked back to his mark visibly distressed.
Kohli was unharmed and went on to score a rousing 115 before Johnson returned to dismiss him late in the day.
"It probably has been a positive thing as well, as bad as that sounds," said Lyon, who took two wickets as Australia battled to hold India to 369-5 in response to their first-innings declaration at 517-7.
"We know the helmets work, and have that confidence for our quicks to have a bouncer again."
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