Holger Badstuber, David Alaba and Luiz Gustavo all picked up yellow cards at the Santiago Bernabeu, thus ruling them out of next month's meeting with Chelsea at Allianz Arena
Holger Badstuber, David Alaba and Luiz Gustavo were booked in the second-leg clash at the Santiago Bernabeu and their mandatory one-game bans mean that they will not be able to face Chelsea at the Allianz Arena next month.
"It is not good that we've lost three of our best players," he confessed. "Badstuber has had an outstanding season, Alaba is very good on the left side and Luiz Gustavo has played very well in the last few weeks.
"They're happy that we have achieved the final but they are also sad. We will miss them in the final."
However, Heynckes was delighted by the resilience his troops had displayed in recovering from the shock of conceding two goals to Cristiano Ronaldo inside the opening 14 minutes to force extra time with a spot-kick from Arjen Robben before then triumphing 3-1 on penalties.
"It was a magical night," the former Blancos coach enthused. "We had big problems in the first 15 minutes, but afterwards my team took over and dominated the match.
"We were sensational - it is a special victory for Bayern."
Robben was also overjoyed with the way in which the Bavarians responded to adversity.
"It was great," the winger enthused. "I'm very proud of my team-mates. When you start a game and you're 2-0 down after 14 minutes you have to be mentally strong to recover.
"The rest of the game we played some really good football and in the end I think it was deserved."
Bayern will be bidding for their fifth European Cup title against Chelsea.