The facility was funded by the "Million for a Morgue" campaign, during which the public donated money to the project while also voting for which crime author to name it after.
The campaign aimed to raise cash to match a Â£1m investment by the university for new facilities.
Ms McDermid said it was a "very proud moment" for her.
The Val McDermid Mortuary, which is now up and running, is the first in the UK to exclusively use the Thiel method of embalming, which it is hoped can provide "significant breakthroughs" in scientific, medical and dental research and training.
A total of 10 authors supported the campaign and were in the running to have the morgue named after them. Each online vote contributed Â£1 to the appeal.
Runner-up Stuart MacBride has had a dissection room at the mortuary named after him, while the other eight authors have had their names put on Thiel embalming tanks.
Ms McDermid had been a keen supporter of the campaign from the outset, having been friends with Prof Sue Black of the university's Centre for Anatomy and Human Identification for nearly 20 years.
She said: "The work that's being done in this mortuary and the knowledge it will communicate means better life chances for all of us.
"For once, we crime writers have had a chance to put life ahead of death and I'm thrilled to have been part of it.
"Million for a Morgue was a mad idea, but it's borne more fruit than any of us could imagine."
Prof Black added that the campaign had been "a tremendous adventure".
"Val is a great friend to the centre and the work we do and so I am truly delighted that the mortuary will be named after her," she said.
"But Stuart has been so pivotal in our success that we have also now chosen to name the dissecting room after him."
The other authors who lent their support were Lee Child, Jeffery Deaver, Jeff Lindsay, Tess Gerritsen, Peter James, Kathy Reichs, Mark Billingham, Harlan Coben and Caro Ramsay.
A new mortuary at Dundee University has been named after crime writer Val McDermid following a public vote.