Having been targeted at a training session earlier in the week, Pique was again the subject of audible jeers when touching the ball early on in La Roja's 3-0 victory against Albania in Alicante on Friday evening, but he left the field an hour in to loud applause.
Asked to comment on the reception Pique received, Lopetegui told reporters: "The fans have been phenomenal. It starts to put the focus on the positive things in our football and our country.
"It is like when you see a painting and you just look at the speck of dust. We have to celebrate the good things and we have done it in the dressing room, singing and dancing."
Pique recently suggested that he has no intention of quitting Spain duty, even if he continues to be jeered by his own fans.