Referee Graham Salisbury waved away Marlon Harewood's appeals after the striker had been felled in the box by substitute Jamie McCombe's clumsy 74th-minute challenge, much to the astonishment of the home side and a crowd of 43,326.
Newcastle caretaker boss Chris Hughton felt it was an "absolute certain" spot-kick, and Johnson added: "I must admit, my heart was in my mouth at the time.
"The lads felt there was a bit of contact but from our point of view, maybe he was starting to go down early, we don't know. But he (Salisbury) was very brave with forty-odd thousand people screaming for a penalty, anyway."
Johnson was delighted with his players, and particularly Dean Gerken, who only discovered he was playing five minutes before kick-off after Adriano Basso picked up a groin injury during the warm-up.
He said: "We made that decision at 2.55pm. I was going to give my super motivational speech and I need them all smiling when I give that, and Basso was grimacing a little bit and doing a stretch on his groin. We were able to bring Dean Gerken in and on the day, I would have thought he was a candidate for man of the match."