Thank you for asking and we can assure you the tradition of bringing in the Sabbath has NO pagan origins or practices! There is no certain scripture that provides for the "proper way" to observe Shabbat, but in a nutshell, here is how candle-lighting came about:
We know that Shabbat is a commanded mo'ed (appointed time) - Genesis 2:3; Exodus 20:8, 20:10. Exodus 20:8 says: "Remember the day, Shabbat, to set it apart for God." Key word - "remember". Deuteronomy 5:12 says: "Observe the day of Shabbat, to set it apart as holy, as ADONAI your God ordered you to do." Key word, "observe".
So, while the Shabbat is a commanded, 7th day mo'ed, the rabbis of old desired a way to do all the requirements of the Sabbath, not only to "cease the work of which you have 6 days", but to remember and to observe! (In Hebrew, the words are "zakhor", and "shamor", the two words actually used in the scriptures.)
Since in the desert, the Hebrews learned to complete their food gathering on the 6th day, because no manna was provided on the 7th day (Exodus 16), and the tradition was born to complete one's work before sunset the 6th day. Thus, the tradition of the lighting of the candles just before sunset! The woman of the house lights the candles because the woman held the role in a Hebrew family of maintaining the activities of the home.
Why two candles? Because one represents the zakhor, and the other the shamor! Why candles at all? Because "the mitzvah is a lamp, Torah is light" - Proverbs 6:23! ... And being a "light" is very important to the Hebrew (Isaiah 49:6). (Because of the commandment not to work on the Shabbat, and not kindle a fire (Exodus 35:3), all other lamps in the home were also already lit before sunset because making a fire in those days was truly hard work. Therefore, any fires, including in the fireplace for warmth, and the Shabbat candles were already kindled before sunset).
The woman brings her hands to her eyes three times because the lit candles now represent the Torah. "Drawing" the light from the flames toward her signifies drawing the spirituality and holiness of Shabbat into her home and into her life. It is done "three" times because according to Jewish tradition, the number three represents commitment and strength. It is also a tradition that the woman holds her hands over her eyes, between her eyes and the candle flame because it represents the intended "creation of the light" AFTER the blessing.
You see, usually, a blessing (Hebrew: berakhah) is given BEFORE an event or activity such as the Kiddush and haMotzi (blessing the wine and bread before a meal). But the candles of Shabbat are lit BEFORE the Shabbat begins (at sunset) so the "work" of lighting the candles is done before Shabbat begins, and the blessing must be said AFTER the candles are lit - so holding one's hands over their eyes to recite the Shabbat blessing is sort of a way to "avoid" the Shabbat light till the blessing is made, and therefore the light is blessed, although after the event! (The origin of saying a blessing before events or activities is a bit obscure, but keeping YHWH "present" at all times is great part of Hebrew/Jewish tradition. See for example Psalm 16:7-8; Psalm 34:1-4; Psalm 64:4).
So the lighting of the Shabbat candles, and the procedures for saying the blessing and the waving of the hands, though largely tradition, is based on many scriptures, and not a pagan practice in sight!