At first, it was customary to perform the Nefillat Apayim prayer by prostrating or by bowing down. Prostration means that the person drops his whole body to the ground, and spreads out his hands and feet. Bowing means that the person gets down on his knees, bends his head forward, and rests it down on the ground (Berachot 34b; Rambam Tefillah 5:13-14).
However, due to a number of concerns, the custom to pray Nefillat Apayim by bowing down or prostrating oneself on the ground was annulled. Some of the reasons are halachic, dealing with the prohibition against prostrating oneself on a stone floor; and the prohibition of an important person falling on his face before the congregation without a guarantee that he will be answered like Yehoshua bin Nun.
Still, the main reason is written in the Zohar (Numbers 121:1), which greatly reinforces the virtue of Nefillat Apayim, during which the person praying must sacrifice his soul to Hashem and view himself as if he has left the world, thereby atoning for all his sins. “This restorative act must be performed with great kavanah of one’s heart. Then HaKadosh Baruch Hu has mercy on him and absolves his sins. Great is the person who knows how to entice his Master and eagerly serve Him with kavanah of the heart. Woe to the one who entices his Master with a distant heart bereft of desire. As it is written (Psalms 78:36-7), ‘They beguiled Him with their mouths and lied to Him with their tongue, for their heart was untrue to Him.’ He says, ‘I lift my soul up to You’ (Psalms 25:1), but his words emanate from a distant heart, and that causes him to leave this world before his time.” Since we are concerned that perhaps we are unable to have the necessary full kavanah and are unworthy, we refrain from prostrating ourselves, or from bowing down.
In practice, it is the custom of all Ashkenazim and some Sephardim to bend down and cover their faces on the shirtsleeve of their arm. By doing so, one maintains a certain aspect of Nefillat Apayim, for that is a type of bow, yet it is not a complete bow, and there is no fear of prostration on a stone floor (Bei’ur Halachah 131:1). Perhaps so as not to encounter the danger mentioned in the Zohar, Ashkenazim were accustomed not to recite the psalm “Eilecha Hashem Nafshi Essa” (“I lift my soul up to You”) (Psalm 25), which is explained in the Zohar to mean the surrender of one’s soul, and instead they recite Psalm 6 (Magen Avraham 131:5). Those who follow the Ben Ish Chai are careful not to fall on their faces at all, and that is how many people from Eidot HaMizrach practice.
. The basis for the prohibition to prostrate oneself on a kneeling stone is brought in Megillah 22b and it is cited by the Rama 131:8. The Mishnah Berurah 131:40 explains that the biblical prohibition entails prostrating oneself on a stone floor, as it is written (Leviticus 26:1), “Do not place a kneeling stone in your land upon which to prostrate yourselves.” This prohibition has two conditions: 1) prostration, and 2) a stone floor. The Chachamim instituted a prohibition even when only one condition exists, meaning that prostration is forbidden even on a floor that is not made of stone, and even just bowing down on a stone floor is forbidden. Chazal do permit bowing down on a floor that is not made of stone. If there are stones there, one may bow by leaning on his side, or by making a separation between his head and the floor, with a towel or the like. Likewise, it is permissible to prostrate oneself on a floor without stones provided that one leans slightly on his side. There is uncertainty as to whether one may prostrate oneself on a stone floor using a separation. See Sha’ar HaTzion 44.
Further, Chazal write in Megillah 22b that a prominent person is forbidden to fall on his face unless he knows for certain that he will be answered as was Yehoshua bin Nun, and that is how the Shulchan Aruch 131:8 rules. However, when he is alone, the Tosafot write based on the Yerushalmi, that it is permissible, and so writes the Beit Yosef in the name of some Rishonim. Similarly, the Mishnah Berurah 38 rules that the prohibition applies when he is the only one falling on his face in front of the congregation, like Yehoshua bin Nun. In a situation such as that one, were he not answered, he would feel ashamed, for those who see him would think he is not worthy. Still, it can be inferred from the Rambam that the prohibition for a prominent person applies even when he is alone. The Meiri explains that this prohibition is to prevent one from considering himself overly pious. See Yad Peshutah on Rambam Tefillah 5:14 where he brings the responsa of Rav Sherira Gaon and Rav Hai Gaon, which implies that when the congregation would prostrate themselves or bow down on the ground, the rabbis would elevate themselves slightly from the floor and turn their faces to the side, and the most prominent rabbis would not bow down at all. Perhaps also for this reason, the custom not to prostrate oneself or bow down, spread throughout the rest of the nation.