With just seven minutes left and United level thanks to Wayne Rooney's equaliser, referee Alan Wiley gave a penalty for Michael Carrick's hand-ball on the advice of his assistant.
That left United manager Sir Alex Ferguson and his players furious, and Ballack with a two-minute wait before he could step up to the spot, taking over the penalty duties from Frank Lampard, who was not playing after the death of his mother.
For the German, however, who had headed Chelsea in front in the first half, it was just the kind of challenge he relishes. He said: "For me, it is no problem, I can handle the pressure. It is always a good situation and I like this. We had just a little chance with a win and we did it."
Ballack had rowed with team-mate Didier Drogba over who should take a second-half free-kick, but he played down any suggestions of a rift, insisting the whole team were fired up for victory.
"Everyone after the game is fine," he said. "Him, me, everyone. It was a great victory and everyone played very strong."
Chelsea manager Avram Grant dedicated the win to Lampard, and was happy with the way his players had taken the game to United. Players held up a Chelsea shirt with the name Pat Lampard and RIP on it after Ballack had opened the scoring late in the first half, and Grant said: "I want to express my sympathy to Frank.
"We thought about him in the game and it's for him.
"In the game, we did what we had to do — we put them under pressure — and we hope we are happy at the end of the season. It's not easy when you are under pressure to win two games."
Grant was particularly pleased with the way Chelsea ground out a win after Ricardo Carvalho's back-pass blunder had gifted an equaliser to Rooney.
He said: "One of our best players made a mistake but this team have a lot of character and we also played good football."
Chelsea face another big hurdle on Wednesday in the Champions League semi-final second leg against Liverpool at Stamford Bridge.
Captain John Terry stoked the fires by branding the treatment his side received from the fans at Anfield last week as 'horrible'.
Chelsea have lost two semi-finals to Liverpool in the last three years, but both times the second leg has been at Anfield, and Terry urged the Stamford Bridge crowd to give Liverpool a taste of their own medicine.
Terry said in his programme column for yesterday's match: "I've got to say that the stick us players took from their fans was horrible, but I'm sure every Chelsea fan will give it back to them on Wednesday night.
"We've heard about their fans around the last two semi-finals and how the second leg at Anfield is to their advantage.
"Well, I'll tell you what I think. Our fans are just as great as theirs when the game's a big one."
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