In my country (Bolivia) is generally believed that the Incas ruling class belonged to a different ethnicity than the rest of the Inca empire. Is there any historical evidence of this assumption being true?

In a way, this is correct. This is mostly due to the nature of it being an empire. The Inca were a cultural group from southern Peru who really start to distingush themselves from neighboring groups during what is called Peru´s Late Intermediate Period, a time of many independent local polities between the Wari (and Tiwanaku) and Inca empires from 1100-1450 AD. Contrary to a lot of laypeople´s ideas that you´ll see, the Inca were hardly the only ones in the Andes at this time. There were the powerful urbanized Chimu in the north coast of Peru, the Pukara folks north of Titicaca in their fortifed hilltop village-fortresses, Aymara kingdoms to the south of Titicaca, ¨Aquillpo¨cultura llama-herders in highland Peru, etc.... Inca rulers, called the sapa Inca, during the 15th century started a campaign of conquest, annexation, alliances, and crafty politics that would craft an empire across the whole Andes. Andean peoples of all varieties were absorbed into the Inca empire, but that didn´t make them Inca. It´s the same as with any other empire. The locals of Judea and Gaul were ¨Roman¨ in the sense that they were under the caesar´s imperium, but they were in no way ethnically Roman.

Now, there is a key difference. The Roman Empire lasted long enough that folks made it all the way to the empire from families in North Africa or Hispania. There wasn´t as clearly defined of a ruling class ethnicity. For the Inca, hereditary right played a huge role, tied in with a deep tradition of ancestor veneration in the Andes. The ayllu is the archetypical Andean organizational unit that is heavily tied to a venerated ancestor(s) and is much political as it is familial. In addition to their default ruling status as conquerors, the hereditary element of politics maintained a distinct Inca class.

TL;DR The Inca were just one of many Andean cultures, who conquered or absorbed other ones into their own empire. They maintained rule through strong hereditary traditions. Think Rome: most people in the Roman Empire weren´t actually even from Italy.

(It so happens that I too am in Bolivia at the moment, so if you want more details on this cursory answer (on ancestor veneration or the like) or have more questions, I´ll be in La Paz with better internet on Saturday.)