After presiding over a startling upturn in fortunes following Andre Villas-Boas' dismissal in February, Di Matteo still doesn't know if he is going to get the job on a permanent basis.
Heynckes sees no reason for further delay.
"I congratulate Chelsea on their victory," said Heynckes.
"If you wish me to say something about Roberto di Matteo it is that Chelsea should give him a three-year contract."
Heynckes admitted his side had no-one to blame but themselves after dominating throughout the 120 minutes.
However, after taking the lead through Thomas Muller with just eight minutes remaining, Bayern allowed Didier Drogba to level in the final minute.
Then, after Arjen Robben had a penalty saved by Petr Cech in extra-time, the customary German efficiency in shoot-out situations failed them as Drogba scored the winning spot-kick to secure a 4-3 triumph.
"Chelsea played the way we thought," said Heynckes.
"We must blame ourselves for having so many goalscoring opportunities without being able to score until the 83rd minute."
Heynckes also confirmed he expected Franck Ribery to shrug off the injury that he sustained in a tackle by Drogba that earned Bayern their extra-time penalty.