Transparency in OpenGL is order dependent. Algorithms exist for order independent transparency, but they are fairly complicated and have some serious compromises. In your case however, you can use alpha testing to solve the majority of this problem. Alpha testing ignores pixels with an alpha below a certain threshold (the empty space in your example). Google it for exact glAlphaFunc usage.
If you are using OpenGL ES 2.0 built in alpha testing is not available, and you must implement it in the shader. It would look something like this:
if (texture.alpha < 0.5)
{
discard;
}
Note that alpha testing may have some serious fill rate performance compromises.