How can I atone for my sin and help my friend out of her situation after having a sexual relationship with her during our university studies?

What you did is a grave sin and a great gateway to evil. It is by Allah's grace that He guided you to repentance and remorse. Therefore, you must persist in seeking forgiveness, feeling remorse, and fearing Allah, while not despairing of His mercy. As for your friend, you must advise her and warn her of Allah's punishment, and you must stop living with her and distance yourself entirely from her unless she repents. You must also adhere to the path of obedience and worship, read the Quran, and associate with righteous girls.