Kohli was struck with the first ball he faced from Johnson and remained unbeaten on 48 with Ajinkya Rahane on 19 at tea.
The tourists were 223 for three and still 294 runs in arrears, after Michael Clarke declared Australia’s first innings at their overnight 517 for seven.
Johnson welcomed Kohli with a bouncer but the Indian captain was OK to continue after a few moments of concern from the fielders. Australia batsman Phillip Hughes was fatally struck by a rising ball late last month, plunging the cricketing world into mourning.
Kohli could not avoid the short-pitched delivery and ducked into the path of the ball which crashed into the front of his helmet.
The Indians only lost the wicket of Cheteshwar Pujara for 73 in the middle session after losing two wickets before lunch.
Pujara missed his chance of a Test century in Australia when he was bowled in unfortunate circumstances by off-spinner Nathan Lyon.
Pujara played a defensive shot, but the ball dribbled off the bat and on to the stumps, ending his 188-minute stay at the crease for 73.
He put on 81 runs for the third wicket with Kohli.
Although Pujara has scored two double Test centuries against England and Australia in India, he has only scored one ton away from the sub-continent with his 153 in South Africa a year ago.
Pujara and Murali Vijay posted India’s highest second-wicket stand at the Adelaide Oval, surpassing the modest 71 put on by Virender Sehwag and Sachin Tendulkar in 2007.
Pace spearhead Johnson struck just before lunch to remove Vijay, who had looked threatening in reaching his seventh half-century with 53 off 88 balls with three fours and two sixes.
Vijay hit the first six of the Test when he advanced down the wicket and slammed Lyon over the long-on ropes and followed up with a four next ball in the 20th over.
He smashed another towering six in Lyon’s next over to keep the Indian scoring rate humming along at more than four an over.
Shikhar Dhawan looked dangerous early, taking 14 off one Johnson over, before Ryan Harris bowled him off an inside edge for 25 off 24 balls in the eighth over.
Michael Clarke spent the first two sessions in the field and made a couple of sprawling saves in the outfield despite his back injury.