A simple slow nod of the head is usually enough to indicate the wine is good/accepted. If there’s a desire to add something vocally, not a bad idea by any mean, a simple “oui” or “c’est bien/c’est bon”, with an optional “merci/merci beaucoup” will do.
If you want to say something, though, articulate slowly and use a warm tone, rather than a quick and dry “merci”, which will likely be interpreted as “please leave us alone now” (the waiter will usually leave without you asking anyway, so pointless to stress one’s desire to be left alone).
As aCOSwt mentioned in comment, if you initially asked for advice on the wine you should have, it would actually be kind to speak out a word of appreciation for the advice once the wine has been tasted (one would actually probably be expected to do so). It can be kept short and yet transmit the appreciation properly: something in the line of “Un grand merci pour votre aide” or “Vous nous avez bien conseillés, merci” would be fine.