yes you could do it by using surface fillets. but beware, they are a little bit tricky. make sure you have the 2nd pipe intersecting the first one completely. because in one of your pictures i saw that both pipes had the same scale and the open end of intersecting pipe wasn´t completely inside the other.

damnit! this becomes really weird right now.. I show you what i mean.

see pic


if you want the circular fillet go all around the intersection maybe scale down CVs from the end of the intersecting pipe.