The Robins trailed to goals from Jamie Mackie and Rory Fallon, and barely managed a shot on target as they were second best in all departments.
A storming fightback saw substitutes John Akinde, with his first Championship goal, and David Noble, with a superb late 25-yard strike, level matters to earn a 2-2 draw, but Johnson was still disappointed.
"That first half was the poorest we have been for some time and probably since I've been here," he said.
"If we had produced another half like that there would have been no light at the end of the tunnel.
"But all our substitutes made an impact and I have to credit the lads for giving it a real go in the second half.
"I thought there should have been more than three minutes of injury-time and if that had been the case we might well have gone on to win it."
Plymouth boss Paul Sturrock urged his players to celebrate the point rather than beat themselves up over City's second-half fightback.
"It's easy to let a draw feel like a defeat when you have been two goals up, but I've told the lads not to think of it like that," said manager Sturrock.
"It was another good away result for us and we would have settled for 2-2 before the game.
"They threw on another big forward for the second half so we knew a lot of diagonal balls would be thrown at us. We panicked a bit at times and it was certainly a game of two halves.
"In the first we looked like scoring with a lot of our attacks and I was really pleased with the performance."
Sturrock admitted he had substituted Fallon in the second half to avoid him being sent off.
"Rory had been booked and received a couple of warnings so it was the only sensible thing to do," he said.
Mackie was the main Plymouth dangerman for 45 minutes.
His shot from just inside the box should have been saved by goalkeeper Adriano Basso, but the goalkeeper could only palm it in via a post for the game's sixth-minute opener.
Twelve minutes later Mackie again escaped the attention of City full-back Jamie McAllister and crossed to the far post where Chris Clark headed down for Fallon to net with an acrobatic volley.
It was all Plymouth until Johnson introduced 19-year-old Akinde in place of summer signing Nicky Maynard at the start of the second half.
Akinde, recruited for a mere £140,000 from Ebbsfleet United, marked his first-team debut with a close-range finish from McAllister's cross in the 63rd minute.
City piled on the pressure and just when Plymouth thought they had weathered the storm Noble came up with a brilliant finish two minutes from time.
The substitute curled his right-footed shot around goalkeeper Romain Larrieu from the corner of the box to send home fans into celebration mood.
Sporting Life