Murali Vijay, who contributed 144 to India's first innings tally of 408, departed for 27, leaving Shikhar Dhawan (26 not out) and Cheteshwar Pujara, who had made 15, to resume on Saturday, 26 runs behind.
Australia had looked to be facing a sizeable deficit of their own when they lost two wickets in the first hour 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 in the same over an hour after lunch but Mitchell Starc (52) 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 Australian batsman to fall but the left-armer returned after the innings break to bowl Vijay when the Indian made the mistake of leaving an angled delivery.
Smith, deputising for the injured Michael Clarke, became the first Australian to score a century in his maiden test as captain since Graham Yallop in 1978.
CAPTAIN'S KNOCK
It was his second century of the series after his unbeaten 162 in the opening test victory in Adelaide last weekend and a fourth in eight matches this year.
"I wanted to lead from the front with my performances so hopefully I've done that so far in this game," Smith told reporters.
"To be fair, our whole tail batted beautifully and to get us up over 500 was remarkable."
It was Johnson's pugnacious 93-ball knock, though, that turned the day in Australia's favour after Indian controlled the first hour and dismissed Mitchell Marsh and Brad Haddin cheaply.
Fired up by some sledging and short balls from the tourists, Johnson 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 century with his 10th four just before lunch, followed five balls later when he chopped on to be dismissed for the first time in the four-match series.
"We tried our best to get them out but you always have this up-and-down phase in cricket and sometimes your strategy doesn't work," India paceman Umesh Yadav said.
"The wicket is a bit slow. It's good for batting now. We will take a good lead and after that we'll see."
(Reporting by Nick Mulvenney; Editing by John O'Brien)
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