So there are three ways that I know of to say this:
Das macht Sinn.
This is what most native speakers would automatically use, as it is a literal translation of "that makes sense". A lot of German people use this as well, as far as I can tell. However, I heard that there was a better variant of it – one that sounded more German or better in German, so I prefer using it myself:
Das ergibt Sinn.
That's good, but I also came across this variant:
Das hat einen Sinn.
I'm not sure where this one fits in.
It might also be different in different contexts. Take this sentence in English for example:
I finished first it by "sliding" on my belly, if that makes any sense.
In this case, which one would I use? This is a slightly different "that makes sense" case, because it's more of an expression in this sentence.