This phrase refers to God the Son. Possible meanings are that 1) the whole phrase simply refers the Son of God and identifies him as God, or 2) the Greek word that is translated here as "only" refers to the only Son of God, and the word "God" is a comment that tells us that the Son is God. Alternate translation: "the only Son, who is himself God"
# the only God
The Greek word that is translated here as "only" is translated by some as "only begotten," which means the only one that comes or procedes from God. The phrases "Son" and "procedes from" can be used to help express some of the meaning of the word "begotten." Alternate translation: "the only begotten God" or "the only begotten Son, who is himself God" or "the only Son who proceeds from God, who is himself God"