As you have rightly mentioned, Shiite Muslims are monotheists and they prostrate for God with the intention to comply with His command. However, Sajdah which is done as a part of some acts of worship such as prayers should meet certain conditions. There is no doubt that those conditions and mandatory rules concerning the Sajdah have not been ordained without wisdom or rationale. One of the conditions as mentioned in the Manual of Islamic Laws (Tauzihul Masail) is that the Sajdah should be performed in the direction of Qibla (Ka'bah):

"The holy Ka’bah, which is situated in Makkah, is the Qibla and wherever one might be he should offer his prayers facing it. However, if a person is away from it and stands in such a manner that people say that he is offering his prayers facing the Qibla, it is sufficient. The position is the same with other acts such slaughtering animals which should be done towards the Qibla."[1]

Also, another condition for Sajdah is that the person who is performing Sajdah should place his forehead on earth or on anything which is a part of the earth or anything that grows out of the earth. It is mentioned in Manual of Islamic Laws as such:

"Sajdah should be performed on earth, and on those things which are not edible or worn, and on things which grow from earth (e.g. wood and leaves of trees).

Sajdah on things which are used as food or dress, or on things which are not considered to be parts of the earth e.g. gold, silver, agate and turquoise is void. However, there is no objection in performing Sajdah on mineral stones such as marble and black stones."[2]

Therefore, a Shiite Muslim believes that he should position his forehead, during Sajdah, on Turbat (clay) which is prepared from pure earth. Observance of these conditions does not imply prostrating for the stone or the Ka'bah itself. Prostrating for stone is a practice of the idolaters. It is shirk (a polytheistic act) and it is therefore forbidden. The difference between Shiite Muslims' prostration and that of the idolaters and pagans is poles apart. Do the idolaters who bow down and prostrate before man-made objects (stones and wood) consider them as a condition for worshipping God or do they consider them as their deities? This is the difference between the prostration of a Muslim and that of an idolater.

Related index:

Question 1111, index: Sajdah of respect for Prophet Yusuf (a.s.).