Matiz translates to "hue" or "nuance." It's a more sophisticated and less common word than simply saying "color," adding a touch of poetic depth to the lyrics.
In the song, Malú sings, "El cielo tiene otro matiz" (The sky has another hue/nuance). This signifies a profound change in her perception of the world since her loved one entered her life. It's not just a different color, but a richer, more complex, and beautiful quality that reflects her newfound happiness.
"Contigo" is Malú and Prince Royce singing about what happens when someone finally makes fear feel small. The verses lay out a person who's spent a long time flinching from love: "Siempre he tenido miedo de quedarme" (I've always been afraid of staying) and later "Siempre he tenido miedo de lanzarme" (I've always been afraid of taking the plunge). Same fear showing up twice, first as refusing to stay and then as refusing to jump in at all.
Then the chorus flips the picture. "Y ahora hay color donde solo había gris" (And now there's color where there was only gray) is the kind of line you either buy completely or you don't, and it works here because the rest of the song backs it up: "Contigo no me duele tanto" (With you it doesn't hurt so much) isn't a claim that the pain vanished, just that it's easier to carry now. By the end they're passing the same image back and forth, "El cielo tiene otro matiz" (The sky has a different hue), "Que se refleja en mí" (That's reflected in me), until the closing line turns it around completely: "Y yo, yo me reflejo en ti" (And I, I reflect myself in you).