When two different types of molecules interact with each other, new substances are created. Baking soda reacts because one of its molecules interacts with another one, and then a chemical reaction occurs.

The baking soda and vinegar reaction is:

NaHCO₃ + H₄CO₂ -> NaH₃CO₂ + H₂CO₃ -> NaH₃CO₂ + H₂O + CO₂

NaHCO₃ is sodium bicarbonate (baking soda)

H₄CO₂ is acetic acid (in vinegar)

NaH₃CO₂ is sodium acetate, a salt

H₂CO₃ is carbonic acid

H₂O is water

CO₂ is carbon dioxide gas

The reason why it bubbles over is the carbon dioxide gas.