I have an embedded google map in my website's homepage. It was embedded using the google maps embed code I got from the maps site.
Whenever I open that page on my iPhone for some reason it opens the google maps app, minimizing the website.
This will happen if you won't use the Google api directly. Don't just embedded the map in your website. Use this great tutorial to make it work: https://developers.google.com/maps/documentation/javascript/tutorial?hl=iw&csw=1
A much quicker solution would be to use google ip 173.194.34.165 instead of google.com in your url. As far as I know the map app won't pick that up.
Use a static map (simple, non interactive) or use the API directly (complicated).
This seems to be a Google "feature".
This is a google feature. You can find more info here https://support.google.com/gmm/answer/3006766?hl=en
I would suggest you to add a link to the map, which when clicked on phone will open the map in google maps app.