Yes, the bible says that God created matter, time, space, logic, physics, etc... out of nothing.
John 1:1-3 ESV In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things were made through him, and without him was not any thing made that was made.
So, with a plain interpretation of the scriptures we see that God literally made everything. You now ask...does that make sense? To that I ask: who made sense? Who made wisdom?
Proverbs 8:22-23 ESV The Lord possessed me [wisdom] at the beginning of his work, the first of his acts of old. Ages ago I was set up, at the first, before the beginning of the earth.
Isaiah 55:8-9 ESV For my thoughts are not your thoughts, neither are your ways my ways, declares the Lord. For as the heavens are higher than the earth, so are my ways higher than your ways and my thoughts than your thoughts.
Romans 11:33 ESV Oh, the depth of the riches and wisdom and knowledge of God! How unsearchable are his judgments and how inscrutable his ways!
You are correct in saying that God making something out of nothing goes against human logic and reasoning--but that's because God created human logic and reasoning and that reasoning is finite. Can you imagine a stick with only 1 end? Can you imagine an all powerful God creating a rock so big he can't lift it? Can you imagine what it's like to be outside of time?
These are just some of the mysteries of God that do have answers, but our brains can't handle them.