Does a bibliography-only citation count like a regular citation for the author?
In the main text, you could also mention the authors by explicitly stating what their tool helped you with, for example:


  Our approach was projected/tested/verified using toolbox Foo (Foosmith 2015) and later ported to C++ for performance measurements.


Apart from thanking the authors, this could also be interesting for the reader.

As the other answers mentioned, a bibliography-only citation counts the same as a regular citation, but such a citation is quite unusual and generally not recommended.