What did the spanish explorers call the Natives of South America (Aztec, Mayan etc.) - was it just the spanish word for "Indian"?

Yes, they called them "indios".

1) "Indio is the Spanish word for "Indian", "Native American" or by mistake Amerindian."

"Indio, Spanish word used mistakenly for Mexicans, Central Americans, and South Americans who are of Indigenous Native American ancestry to whatever degree (see Indigenous Mexicans). It was also used in Spanish Colonial times for the ethnic Malays in the Philippines, who were not called Filipinos in Spanish Colonial times. Filipino Sailors serving in the Manila-Acapulco Galleon Trade were called Luzones Indios, Manilamen, or Indios Bravos in the Philippines and Mexico in colonial times. The name “Filipino” was given to the white Spanish colonists born in the Philippines. Particularly in South America, the word Indio may be used in a derogatory point of view from members of a different ethnic group."
Source and further information:
http://en.wikipedia.org/wiki/Indio


2) "The indigenous peoples of the Americas are the pre-Columbian inhabitants of the Americas, their descendants, and many ethnic groups who identify with those peoples. They are often also referred to as Native Americans, First Nations and by Christopher Columbus' historical mistake "American Indians" or "AmerIndians"."

"Application of the term "Indian" originated with Christopher Columbus, who thought that he had arrived in the East Indies, while seeking India. This has served to imagine a kind of racial or cultural unity for the aboriginal peoples of the Americas. Once created, the unified "Indian" was codified in law, religion, and politics. The unitary idea of "Indians" was not originally shared by indigenous peoples, but many now embrace the identity."
Source and further information:
http://en.wikipedia.org/wiki/Indigenous_peoples_of_the_Americas


3) "In South America, like in Mexico, the preferred expression is Indigenous Peoples (pueblos indígenas in Spanish, povos indígenas in Portuguese). However, Indians (indios, índios) is often used too, even by indigenous peoples themselves, since this expression is not seen as derogatory."
Source and further information:
http://en.wikipedia.org/wiki/Native_American_name_controversy#South_America


4) Further information, if you understand spanish:
http://es.wikipedia.org/wiki/Ind%C3%ADgenas#El_t.C3.A9rmino_.C2.ABindio.C2.BB
http://es.wikipedia.org/wiki/Amerindio