The decision follows widespread criticism of Yorkshire's handling of a report which found Mr Rafiq had been a victim of racial harassment and bullying while at the club and recent reports that the investigation had dismissed him repeatedly being called a 'P****' as "banter".
The club has said no disciplinary action against any employee is planned, while on Wednesday night current player Gary Ballance admitted he had used "a racial slur" towards Rafiq when they were team-mates at Yorkshire.
In a statement this afternoon, a spokesperson for the sportswear giant said: "Nike will no longer be the kit supplier for Yorkshire CCC. We stand firmly against racism and discrimination of any kind.”
Nike signed a four-deal kit sponsorship deal with Yorkshire earlier this year.
Harrogate Spring Water also announced it was ending its partnership with the club.
The company said: "We were deeply concerned at the details that have emerged in recent days surrounding the treatment of Azeem Rafiq at Yorkshire County Cricket Club and the way in which the club’s current leadership have handled the important issues that have been raised.
"As a result, Harrogate Spring Water has taken the decision to end its sponsorship agreement with the Club with immediate effect."
Leeds Beckett University said it was "pausing all currently planned activity" with Yorkshire.
A spokesperson said: “Leeds Beckett University stands united against racism, and in our support for anyone who experiences racism.
“Although the issue is complex and we are not in possession of all the details, Yorkshire County Cricket Club’s public statements to date suggest that its approach to the handling of these accusations is inconsistent with our values and culture.
“The university is pausing all currently planned activity with YCCC with immediate effect. There is no current financial sponsorship arrangement between the university and the club, and the university logo has been removed from the club website at our request.
“Our future relationship with YCCC will depend on what emerges from the ECB review and the evidence of meaningful change that the club commits to, to end racism. If it can do this, as we are seeking to do ourselves, then we would hope we can work together on a partnership that plays a positive role in our community in the future.
“We will continue to maintain a dialogue with the club about its approach to this issue.”
Vertu Motors has also decided to end its sponsorship deal - but said the decision "could be revisited if new leadership takes the club in a new direction".
A spokesperson for Vertu Motors said: “One of the core values of our business is respect. We are obviously concerned about the issues that have been widely reported this week.
“We are disappointed in the way this matter has been handled by the leadership at YCCC, which has not given us confidence that its values align with our own.
“We have taken the decision to end our sponsorship, a decision that could be revisited if new leadership takes the club in a new direction.”
It follows Headingley stadium sponsor Emerald Publishing cutting ties with the club earlier this week, with similar decisions announced by Yorkshire Tea, David Lloyd Clubs, Tetley's Beer and Anchor Butter.
Another club sponsor said today they were awaiting further information before making decisions on their future involvement with Yorkshire.
A Sodexo spokesperson said: “Sodexo has a long-standing commitment to fairness and equity and is dedicated to creating a diverse and inclusive workplace. As the hospitality partner for Headingley Stadium, we have written to the Club this week on this very serious matter. We are keen to understand the steps they will be taking."
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