The Spanish side were heading out of the competition as they trailed Paris Saint-Germain 3-2 on aggregate following Javier Pastore's 50th minute strike when Messi, who suffered a hamstring injury in the first leg, was thrust into the fray.
He immediately transformed a previously tentative home side and the equalised nine minutes after his introduction when the Argentina ace unlocked the PSG defence to find David Villa, who rolled the ball back into the path of Pedro to lash home.
Central defender Pique told Sky Sports: "We are talking about the best player in the world. It doesn't matter if he is a little bit injured, he can change everything and he did again.
"We are really lucky and really proud to have Leo on the team and we have to use him when we are struggling a little bit.
"We knew that for us to have Leo on the pitch was really important. He is our reference, he can score he can pass, he can do everything and he helps us a lot.
"If you have him you have to use him and try to use the best part of him and he helped us a lot."
Barcelona's away goals victory made them the first club to reach the semi-finals of the Champions League for six successive seasons, and Pique is happy to face any of Real Madrid, Bayern Munich or Borussia Dortmund in the last four.
He added: "This club has shown a lot of quality in the last six years. We deserve to be in the semi-finals for one more year. It was really tough and really difficult because they are a strong team, with good quality.
"We are really happy to have qualified for the semi-finals. I don't care who we play, the most important part is to be there. The German teams are really strong and Madrid is one of the best in history.
"It will be tough, but we are in the semi-finals and you expect this when you arrive here."