The one-off Test was supposed to start on Monday but the toss is yet to take place because of rain and the poor condition of the Greater Noida ground
The tall 26-year-old Queenslander flourished in his maiden Test on Indian soil as the hosts, replying to Australia's first innings total of 430, groped to 133-4 by lunch.
Rahul Dravid was at the crease on 35 and fellow veteran Sourav Ganguly, who retires after the four-Test series, was on seven.
It was a session of gripping cricket as Johnson and Brett Lee made India's batsmen struggle on a dual-paced wicket where deliveries rose alarmingly or keep low at times.
Sachin Tendulkar, needing 77 runs to overtake retired West Indian Brian Lara as Test cricket's highest run-getter, was dismissed for just 13.
India lost the overnight pair of openers Gautam Gambhir and Virender Sehwag within the first five overs after the hosts resumed at 68 without loss.
Gambhir was trapped leg-before by Lee for 20, while Sehwag edged a wide ball from Johnson to lone slip Matthew Hayden after making 45.
Tendulkar, playing his first competitive match since the Test series in Sri Lanka in August due to a shoulder injury, was greeted by a ear-splitting roar from 25,000 home fans at the Chinnaswamy stadium.
He opened his account by slashing Lee to the point boundary, but was lucky to survive the next over when he was stranded down the wicket as Michael Clarke's throw narrowly missed the stumps.
Tendulkar had another escape before he had reached double figures, pushing a short ball from Johnson just out of the reach of debutant Cameron White at short point.
Johnson, however, had the final say as Tendulkar patted a slower delivery straight to White in the same position to reduce India to 94-3.
Cricket-India v Australia - 3rd day, 1st test, lunch scoreboard
Australia first innings 430 (R. Ponting 123, M. Hussey 146, Z. Khan 5-91)
India first innings (overnight 68 for no loss)
G. Gambhir lbw b Lee 21
V. Sehwag c Hayden b Johnson 45
R.Dravid not out 35
S.Tendulkar c White b Johnson 13
V. Laxman c Haddin b Johnson 0
S.Ganguly not out 7
Extras (b-5, lb-4, nb-3) 12
Total (for four wickets; 42 overs) 133
Fall of wickets: 1-70, 2-76, 3-94, 4-106
To bat: MS Dhoni, A Kumble, Harbhajan Singh, Z Khan, I Sharma
Bowling: B Lee 11-3-27-1 (nb-1) S. Clark 10-2-37-0, M.Johnson 13-3-42-3, S. Watson 7-2-11-0 (nb-2), C. White 1-0-7-0
The one-off Test was supposed to start on Monday but the toss is yet to take place because of rain and the poor condition of the Greater Noida ground
Afghanistan has hosted several Twenty20 and one-day internationals at Greater Noida since 2017
Warner, who retired from international cricket, will play for Bulawayo Braves Jaguars
It was their fourth victory in 21 Tests in England over 40 years and their first since a 1-0 victory in a two-Test series 10 years ago
The visitors seem set to claim victory on Monday, barring yet another twist in a Test match full of them
Virat Kohli also returns to the Test team after he missed the five matches against England at home due to the birth of his second child
The first Asian-origin cricketer to captain England in T20Is, Ali has scored five centuries in tests and three in ODIs, also taking 366 wickets across all three formats
The former all-rounder has returned to cricket during the past year after a horrific car crash at the end of 2022