If you read the Holy Quran, you will find that "Huwa" (He) is used for Allah. The reason for this is very simple and anyone who has studied Arabic grammar would be able to know it.
In Arabic grammar, there are two pronouns whereas in English there are three. English has a masculine pronoun (he), a feminine pronoun (she) and a neutral pronoun (it). However, Arabic has only two pronouns, masculine (Huwa) and feminine (Hiya). These two Arabic pronouns are also used for the neutral pronoun. However, to use the feminine pronoun as a neutral one there are some restrictions such as the thing should be regarded as feminine by the Arabs. However, for those things which do not pass these restrictions Huwa is used. That was the case with the word "Allah" so Huwa (neutral pronoun) is used.