Messi's stoppage-time spot-kick was saved by Manchester City goalkeeper Joe Hart at Etihad Stadium, although Barcelona still triumphed 2-1 in the round of 16 first leg to take a significant step towards the Champions League's last eight.
Although the penalty would have given Barcelona a two-goal cushion ahead of the second leg on March 18, Suarez was not convinced it would have "killed off" the tie, while Luis Enrique claimed victory was the most important thing.
"This was a very good display from our team, we were much better than our opponents," Barca's coach said.
"We played a very complete game and we should be very satisfied with that. The aim was always to win the game, we did not care too much about the precise result.
"We have to bear in mind the quality of our opponents and how difficult this tie is."
Luis Enrique added: "Players who take penalties will always miss some but we have full confidence in [Lionel] Messi."
Suarez had given the visitors a 2-0 lead at half-time with a pair of fine finishes in Manchester - his first brace for Barcelona - while Sergio Aguero struck back for City in the 69th minute.
The Uruguayan striker took his tally to four goals in Barcelona's past five matches and he backed the La Liga outfit to hold off City at the Camp Nou.
"We played really well in the first half," Suarez said.
"They're a great side with a lot of quality in midfield and up front. It's still open going into the second leg but we're Barca."
Messi won a penalty with full-time approaching but, after taking responsibility from the spot, his effort was saved by Hart and the Barca legend's follow-up diving header went wide of the post.
Suarez said: "I don't know if it [Messi's penalty] would have killed off the tie. These things happen."
