Messi scored a brace and set up Ousmane Dembele as the La Liga giants beat Chelsea 3-0 in their last-16 second leg, completing a 4-1 aggregate win.
The Argentina star was thrilled to get to the milestone and was pleased his team managed to move into the last eight.
"I'm happy to have reached 100 goals in such a beautiful competition, but the important thing was to move forward in a difficult match against a team with lots of really good players," Messi told UEFA.
"We managed to score early and this was important. I'm happy with how it all happened.
"This was a tough match and we were strong as a team. When we scored the third then the tie was practically ours."
Chelsea head coach Antonio Conte lauded Messi post-match, saying the 30-year-old was the world's best and made the difference in the tie.
Messi was appreciative of the Italian's comments, but his focus was on his side progressing.
"I didn't hear him, but they told me what he said and I thank him for his words," he said.
"I am happy for how this night has ended and for reaching the quarter-finals, which is what we wanted."