Yes it does. It is called a Super GPU server, but on the product page, you will see it supports GPU/MIC cards in the PCI-E 3.0 slots. Xeon Phi's are sometimes referred to as MIC since they have Many Integrated Cores (MIC).
On the product page, http://www.supermicro.com/products/system/1u/1017/sys-1017gr-tf.cfm, there is also a Compatible GPU List. The Xeon Phi is listed on there for your convenience (even though it is not technically a GPU).
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