The Souths winger entered the history books during the first set after half-time, when a break down the left edge ended with his 213th career try, and second of Friday's sold-out game.
Johnston had earlier grabbed a Latrell Mitchell flick pass to score his first try of the night and equal Ken Irvine's mark of 212, which the legendary winger set in 1973.
Security presence was increased for the round-two clash after Souths players and coach Wayne Bennett had this week urged supporters not to invade the pitch.
But fans were undeterred by the prospect of $5,500 fines, having booed earlier in the game when the big screen displayed warnings against entering the field.
The majority took around five minutes to return to the stands as the ground announcer reminded the crowd that "we've got a game of rugby league to play".
Prime Minister and devoted Souths fan Anthony Albanese was among those on the field celebrating rugby league history being made.
Players took refuge in the dressing sheds amid the chaos as a handful of the more sluggish supporters were detained by security and police.
Sporting a new jersey with a golden No.2 on its back, Johnston applauded and waved to the crowd when the teams returned to the pitch.
Play resumed roughly 15 minutes after his try had helped Souths level the scores at 12-12 and sparked the momentous scenes in the northern in-goal.
In commentary for Fox Sports, NRL legend Cooper Cronk called Johnston's feat "the greatest moment in our game's history for a long period of time".
But Johnston's unforgettable effort wasn't enough to prevent the Roosters bouncing back from their hefty round-one loss, with a narrow win on Friday in front of 41,424 spectators.
Around 10 minutes after the resumption, the Roosters shifted right to reclaim the lead through Johnston's opposite man Mark Nawaqanitawase, who narrowly remained in the field of play as he planted the ball down.
A Sam Walker penalty goal had the Roosters eight points in front, before Jack Wighton poked a kick through the line for Campbell Graham.
Mitchell's sideline conversion put the Rabbitohs back within two, before James Tedesco sealed the win by planting Daly Cherry-Evans' grubber down in the final minute.
Cherry-Evans had earlier opened the scoring by stepping inside for his first try in Roosters colours.
A moment's silence was observed prior to kick-off, at the Roosters' first home game since the Bondi Beach terror attack, which took place less than 5km away, in December.
