Phillips was suspended pending an investigation into social media posts he made after the group marched through London on October 13.
The DFLA, who have self-proclaimed themselves as an "'anti-extremist' movement" have been heavily criticised by anti-racism campaigners in the past.
West Ham launched an investigation into his social media posts in which Phillips defended the group after violence erupted during the march.
He tweeted: “The football fans were sticking to the agreed route and Antifa chose to confront the march. They had their face covered up. We didn’t. Ask yourself who instigated the trouble?”
But an inquiry found that his posts did not bring the club into disrepute and believe they don't have valid grounds to give him the sack.
A club statement read: "West Ham United can confirm that following suspension and subsequent investigation, academy coach Mark Phillips has been reinstated to his role in accordance with employment law, and has been reminded of his responsibilities."
Phillips works as a coach for the club's under-18 side and has reportedly been handed a final warning.
He will now continue his coaching after attending courses on discriminatory issues and bias, which is compulsory for all West Ham employees.
The march in October descended into violence when anti-fascist demonstrators blocked the route.
There is no suggestion Phillips was involved in the disorder.
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