Nathan Redmond, who played a key role in England Under-21s’ 3-2 win over Germany on Monday, came off the bench to set up Johnson for his 11th goal of the season as the Seagulls lost at home for the first time in five outings.
Norwich – who move up to third, for a few hours at least – have now won nine of their last 13 games.
Hughton brought in Inigo Calderon for Emmanuel Ledesma as he faced his former employers for the first time since being sacked as Canaries boss a year ago with their relegation from the Premier League becoming inevitable, while counterpart Alex Neil had the luxury of naming an unchanged side.
Johnson’s fierce free-kick was parried behind by David Stockdale in the third minute, while moments later Chris O’Grady tested John Ruddy with a low shot after being played in by Calderon.
The visitors’ midfield soon began bossing affairs with the experienced trio of Alex Tettey, Johnson and Graham Dorrans dominating proceedings.
But despite stroking the ball around with the sort of confidence expected from a side who had lost just once in their previous 12 matches, the away side struggled to create chances – although Wes Hoolahan might have done better when he was played in by Cameron Jerome after Gordon Greer’s mis-kicked clearance.
A dangerous drilled Martin Olsson cross somehow evaded everyone and Johnson’s improvised effort from 30 yards drifted wide, before Brighton enjoyed a late surge towards the end of the first half.
Sebastien Bassong’s woeful back-pass after 38 minutes let in Beram Kayal, but he opted to pick out Joao Teixeira when he might have shot himself and the chance passed.
Portuguese midfielder Teixeira then wriggled free in the box only for his low cross-shot to be scrambled away, and the Liverpool loanee’s shot in first-half stoppage time was kicked away by Ruddy.
Brighton felt they should have had a penalty shortly after the restart when Teixeira went down under Bassong’s challenge, but referee Andy Davies correctly waved play on.
Canaries boss Neil introduced Redmond, who scored the equaliser on Monday before James Ward-Prowse poached a late winner, 10 minutes after the break and the right winger made an instant impact when he skinned full-back Joe Bennett and cut the ball back for Johnson to fire home from 12 yards.
Hughton introduced the attacking trio of Kazenga LuaLua, Craig Mackail-Smith and Leon Best, and, although LuaLua’s cross almost found Mackail-Smith seven minutes from time, they could not manage the same impact as Redmond and Norwich comfortably closed the game out.