"Journée" is used because it means "day". When you are talking about the entire day, "journée" is used.
J'ai eu une journée fantastique hier!
I had a fantastic day yesterday!
"Jour" has many uses; it can describe "day and night", for example when the sunbeams enter in your bedroom in the morning, and wake you up!
It can also be used to talk about a date.
Day and night:
Il fait jour!
It's daylight!
Il fait nuit!
It's dark!
Date:
Un jour, je le ferai.
One day, I will do it.
Je le ferai ce jour-là.
I will do it this day.
Keep in mind that "jour" has other uses depending on the context.
Hope that helps.