Heynckes is in his fourth spell at Bayern, with his third ending with victory in the 2013 Champions League final.
To repeat that feat, he will have to find a way to overcome defending champions Real in the semi-finals, with the German club at home in the first leg on Wednesday, 25 April and then travelling to Madrid on Tuesday, 1 May.
Real, who have won the competition in three of the past four seasons, reached the last four by coming through a dramatic second leg against Juventus.
Leading 3-0 from the first tie, Zinedine Zidane's side were pegged back to 3-3 at the Bernabeu, before a last-gasp penalty from Cristiano Ronaldo saw them through.
Zidane has been under pressure this season though, particularly for his team's league form, with Los Blancos fourth in La Liga and 15 points behind leaders Barcelona.
Real beat Bayern in a dramatic and controversial quarter-final last season - winning 6-3 on aggregate after scoring three goals in extra time - on their way to lifting the title.
"It's one of European football's top clashes. It's the defending champions against a top side with quality players," said Heynckes.
Arsenal handed tough draw
Arsenal won their quarter-final against CSKA Moscow 6-3 on aggregate, but were made to work in Thursday's second leg.
Leading 4-1 from the first tie, the Gunners conceded twice in Moscow and needed late goals from Danny Welbeck and Aaron Ramsey to make progress more comfortable.
Winning the Europa League looks to be the Gunners' most likely way of qualifying for next season's Champions League, with Arsene Wenger's side sixth in the Premier League and 13 points adrift of fourth-placed Tottenham.
Atletico, Europa League winners in 2010 and 2012, are considered favourites to win the competition and are second in the Spanish La Liga, 11 points behind leaders Barcelona and with the best defensive record in the league.
They came through their semi-final against Sporting Lisbon 2-1, losing the second leg 1-0 in Portugal.
What are Liverpool's chances of winning Champions League?
Data analysts at the Euro Club Index, along with Simon Gleave, head of analysis at Gracenote Sports, have simulated the remaining fixtures and given Liverpool a 60% chance of reaching the final and a 20% chance of winning the competition outright.
They rate Real and Bayern both at 50% to reach the final, but give the Spanish team the edge to win the competition with a 35% chance compared to the Bundesliga club's 34.5%.
Arsenal are given only a 30% chance of progressing past Atletico Madrid and are at 19% to win the competition.