Which substance found in fossil fuels can form a harmful acid when the fuel is burned?

Answer is: sulfur.

Fossil fuel combustion increases the acidity of rain because the sulfur dioxide is produced.  

Because of fuel combustion, sulfur dioxide goes up into the atmosphere as the hot gases rise, than it reacts with water and oxygen in the air and form sulfuric acid:  

Balanced chemical reaction: SO₂(g) + 2O₂(g) + 2H₂O → 2H₂SO₄.  

pH (potential of hydrogen) is a numeric scale used to specify the acidity or basicity an aqueous solution.

When pH is less than seven (pH<7), solution is acidic.