A 3-0 triumph at the Camp Nou last night sealed a 7-0 aggregate victory for the Bavarian outfit.
Blaugrana have widely been regarded as Europe's best team in recent years, but Heynckes does not believe that their team is now in demise.
"I wouldn't say we witnessed the end of an era tonight," Heynckes told UEFA.com.
"Barcelona were missing a lot of players and we put in a clever performance.
"My team understood our tactical approach very well and they executed it perfectly. Our organisation was superb."
Bayern take on Bundesliga rivals Borussia Dortmund in the final at Wembley on May 25.