The 67-year-old coach hailed his side's "clever" performance on Wednesday night, but feels they were fortunate not to have had to contend with the Argentine ace
The Argentine watched on from the substitutes bench as Arjen Robben's stunner, a Gerard Pique own goal, and Thomas Muller's late strike condemned his side to a 7-0 aggregate defeat in the Champions League semi-final.
And while Heynckes was proud of his team's focus in the tie, he acknowledged the Blaugrana are a different prospect without their talismanic attacker.
"I think it was clearly noticeable that my team entered this game extremely focused," he told reporters after the match. "We played great right from the start. However, there is no denying it – Barcelona is a different team without [Lionel] Messi.
"Still, I am sure no one expected us to win 7-0 on aggregate. I would not say that we witnessed an end of an era tonight. Barcelona were missing a lot of players and we showed a clever performance."
Bayern will now contest the final on May 25 against Bundesliga rivals Borussia Dortmund, and Heynckes feels BVB's place at Wembley is fully deserved, albeit a little surprising.
"Dortmund deserve to be in the final, as they are playing a great season as well," he continued. "Sure, it is a small surprise that they reached the final. I obviously hope that we can be successful in Wembley. We will now reflect on what we achieved tonight, enjoy the moment and then put our focus on the game against Dortmund on the weekend [in the Bundesliga]."
Much has been made of the future of Heynckes as the arrival of Pep Guardiola draws ever closer, but the 67-year-old has stressed there has been no contact with Real Madrid over a possible return to the Santiago Bernabeu.
"Madrid have not been in contact with me," he remarked to Marca after Wednesday's match.
"On May 9 I turn 68, I think I should be thinking about taking a break."