Australia had looked to be facing a sizeable deficit when they lost two early wickets to slip to 247/6 but Smith and Johnson combined for a Gabba record seventh-wicket partnership of 148 runs from 160 balls.
Both fell to paceman Ishant Sharma (3-117) in the same over an hour after lunch but Mitchell Starc continued the resistance with his fourth Test half century and partnerships of 56 with Nathan Lyon (23) and 51 with Josh Hazlewood (32 not out).
Starc was the last batsman to fall, bowled by Ravi Ashwin for 52 four balls after the delayed tea break.
Smith, deputising for the injured Michael Clarke for the remainder of the series, became the first Australian to score a century in his maiden Test as captain since Graham Yallop in 1978.
It was his second century of the series after his unbeaten 162 in the first Test victory in Adelaide last weekend and a fourth in eight Tests this year.
It was Johnson's pugnacious 93-ball knock, though, that turned the day in Australia's favour after he arrived at the crease an hour into play with his team tottering and well short of India's tally of 408.
Fired up by some sledging from the tourists, the paceman stopped the rot in no uncertain fashion by clubbing the ball around the ground with 13 fours and one six.
The lefthander looked to be heading for his second Test century when he chased an Ishant delivery only to get a top edge which Mahendra Singh Dhoni snaffled up behind the stumps.
Smith, who had brought up his sixth Test century with his 10th four through the covers just before lunch, followed five balls later when he chopped on to be dismissed for the first time in the series.
For the first hour, however, it had looked like being India's morning after an Ishant inswinger bowled Mitchell Marsh for seven and Brad Haddin fended a short Varun Aaron delivery straight to Cheteshwar Pujara at short leg for six.
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