The German club edged out Malaga in a thrilling and controversial 3-2 victory at Signal-Iduna Park in the second leg of their quarter-final tie thanks to two stoppage-time goals.
However, the Serb admits that his side were not in their best form during the contest.
"It was definitely not our best game, we were playing too slow, we didn't create many chances in the first half and did not get to play our football," Subotic told Sky Sports News.
"Malaga know how to play defensively and they did a good job of that.
"I don't care if it was deserved or not, it's about taking it. Our story this season has been like a Hollywood movie, I hope it has a Hollywood ending."
The triumph means that Dortmund have reached the semi-finals of Europe's elite competition for the first time since they won the trophy back in 1997.