Simply check the engine number. If it is 1KR-FE it is 1000 CC. If it is 2NZ-FE or 2SZ-FE then it is 1300 CC.
1000 CC vitz has 3 valve engine. So you can seen three valves on the top. But 1300 CC has four valves.
This is 2SZ-FE engine of my vitz. It is 1300Cc. You can see one head. And other three heads are under that black air intake box.
And this is 1KR-FE engine. It is 1000CC. By the way this ride belongs to @ajjubravo bhai. Ajjubravo bhai has changed his air intake and the three heads are clearly visible.
With Company fitted air intake the 1000Cc engine will look like this (No heads visible):