With the numerical advantage Derby dominated, but couldn't find the crucial breakthrough until the 85th minute as Gary Teale attacked a back-stepping City defence from the left-wing and found the back of the net with a well-struck right-foot shot, much to the relief of the lions' share of over 27,000 fans.
And Johnson lay the blame largely at the feet of his ill-disciplined skipper.
He said: "Over the years he's been a real stalwart for us and that's why he's captain, but today he was petulant and unprofessional.
"He needed to keep his wits about him and not get involved in any petulance, but he did.
"He's apologised and he will do because he's a decent lad, but obviously he's let his team-mates down today and he knows that."
However, despite creating some good early chances, two of which were spurned by on-loan striker Alvaro Saborio, Johnson conceded that Derby deserved the three points.
"I was disappointed that we weren't 1-0 up with the first attack, but I wouldn't take the victory away from Derby."
Rams boss Nigel Clough hailed his side's narrow victory, which at times looked in doubt as his players repeatedly squandered chance after chance.
Derby, who had new loan signing Fredrik Stoor on the bench, were caught napping early on as Saborio missed a sitter with a weak header from six yards but improved as the game progressed with James Vaughan, Rob Hulse and Dean Moxey all coming close to scoring.
Fifteen minutes into the second period, the balance of the game was tipped heavily in the home side's favour as McCombe saw red and with the Robins reduced, the Rams dominated completely for the remaining half hour.
Lee Croft should have broken the deadlock but fired wide of an empty goal before Paul Dickov failed to hit the target from six yards out not once but twice. But the crucial strike finally came with just five minutes of normal time remaining as Teale found some space and beat Basso in the Bristol goal.
And it was the tenacious attitude of his players that most impressed the Rams boss Clough.
"We kept going and we kept playing and trying to do the right things," he said.
"If you've created chances for 85 minutes, you're going to keep creating them if you keep going.
"It is a relief of course, but it was deserved again. I thought the performance was very, very good indeed but not too different to how we've played in recent weeks - it's just nice to get what we feel we deserve."