Which pre-Columbian civilization invented a zero before Europe used it widely?

The Maya, who had a positional number system with a symbol for zero - usually a shell glyph - by at least the fourth century AD and probably earlier, developed entirely independently of the Indian zero that reached Europe through Arabic mathematics.

They needed it for the calendar. Maya astronomy tracked Venus with an error of about two hours over five hundred years, and the Long Count records dates by counting days from a fixed origin - which requires place value, and place value requires a symbol for an empty column. Their arithmetic was base twenty rather than ten, probably from counting fingers and toes.

Nearly all of the writing is gone. Three or four codices survive, out of what must have been thousands, because a Spanish bishop burned the libraries of the Yucatán in 1562 - Diego de Landa wrote that they contained nothing but superstition and lies of the devil, that he burned them all, and that the people regretted it to an amazing degree. The same man then wrote a description of Maya writing that turned out to be the key to deciphering it four centuries later.