Heynckes won Europe's premier club competition in his only season in charge at Real in 1997/98 and it was a triumphant return to the Bernabeu for the 66-year-old German.
Bayern looked to be heading out of the competition, in which they were losing finalists to Inter Milan at Real's stadium in 2010, when Cristiano Ronaldo put the Spaniards 2-0 ahead inside the first 15 minutes of Wednesday's semi-final second leg.
But they gradually got into their stride, Arjen Robben netting a 27th-minute penalty to make it 2-1 on the night and 3-3 on aggregate before goalkeeper Manuel Neuer saved spot kicks from Ronaldo and Kaka in a dramatic shootout to help the Bavarians through to the May 19 final.
"We had big problems in the first 15 minutes and then we played some excellent football for long periods," Heynckes said.
"I am particularly happy for my players and all the people who work for the club."
If Heynckes was the architect of Bayern's success, keeper Neuer was the hero on the ground, denying the two former World Players of the Year with athletic dives low to his right to block their spot-kicks.
"We have all worked very hard for this," the 26-year-old said.
"In both games we went toe to toe with Real at the very least and we were deserved winners in the end.
"I wanted to save the penalties at all costs. Luck of course plays a part."
ONE GOAL
Although Real keeper Iker Casillas revived Real's hopes by denying Toni Kroos and Philipp Lahm in the shootout, Sergio Ramos's wild shot over the bar paved the way for Bastian Schweinsteiger to score and send Bayern through.
"We are all dead but exceptionally happy," the Germany international said.
"Since we knew the final was going to be in Munich we all had one goal: to get there," he added.
As well as the Champions League title, Bayern also have a chance to win the German Cup when they meet newly-crowned Bundesliga champions Borussia Dortmund in the final in Berlin on May 12, a week before they host Chelsea.
