A shambolic first-half acted as a wake-up call ahead of next Friday's trip to Sheffield United in the first leg of their play-off semi-final.
Johnson said: "You've got to try and go into your play-off games seeing your game. Our game is what has got us this far, but we didn't recognise our game.
"We were playing like individuals rather than a team and lost all thought of what we are trying to achieve.
"But second half we went out and became a bit more relentless and should have drawn.
"It was a really poor first half and we can't afford a half like that in the play-offs, so maybe it's a warning not to go into the play-offs complacent.
"Our win at Bramhall Lane earlier in the season was one of our best and we're going to need that type of performance again because it's going to be like the play-off final up there.
"There will be 35,000 Sheffield fans getting behind their team and we've got to go up there and make sure we don't choke."
Jonson Clarke-Harris volleyed Bury into an early lead and added a second with a stunning 20-yard free kick. Nicky Ajose then made it 3-0 with a quality finish.
Yeovil woke up after half-time, James Hayter heading home from a corner and Kevin Dawson adding a second in injury time.