"The enormous amount of love and respect that we have for each other will only increase as we move forward", they added.
Us Weekly also reports that the couple have been separated for a couple of months now, although an exact date is unclear.
The couple said in a statement to Us Weekly on Tuesday their decision to separate was a joint effort and that they will remain friends.
It comes after the "OMG" hitmaker was hit by a $20 million lawsuit in August previous year from two women and a man who claimed he had put them at risk of the sexually-transmitted disease. Though that case was later dismissed, Usher has previously settled another case with a woman for $1.1 million.
The woman alleged she contracted herpes when she had sex with Usher in a Los Angeles spa.
Grace stood by her man throughout the scandal.
The Brooklyn-bred Miguel brushed off the legal drama in November, telling TMZ, "People are people, living their lives". Sources also told the site Grace was unbothered by the allegations and wasn't "giving the lawsuit [s] any weight".
The short-lived marriage only represented a small part of the couple's relationship.