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A check online shows that, technically, abortion is illegal in Germany.
However, the criminal code states that within the first 12 weeks of conception a woman can get an abortion if she takes part in a government mandated counselling session.  This counselling session needs to be carried out by a doctor at least 3 days before the abortion and is done "to protect the unborn child". The counselling is obligatory.

Late abortions are allowed if the physical or mental health of the mother is at risk.

You need to both go to a doctor to start the procedure and to get information on how it all happens.

First, let me say: A woman's cycle is variable and two days late is no reason yet to worry. Wait a few more days, then get a pregnancy test kit, available cheaply from any pharmacy!
If that is positive, she should visit a gynaecologist. There she can probably also get more information about abortion. In case she can't, here is some information I gathered (as you are not the first one I advice about this on the forum):
1. Killing an unborn child is not a decision to be taklen lightly! There is sufficient support available in Germany to enable anyone to rear a child in almost any circumstances. And while some effect on your studies is probably inevitable, the joy of having a baby will more than make up for it.
2. If you do decide for an abortion, you need to get a mandatory counselling session first (as Stumpy stated above). I recommend a charity organisation like "Pro Familia" for that. They have offices in all major cities (see ).
3. After counselling and a minimum 3 days time for consideration, you can get the operation at a specialized abortion clinic. These clinics are not allowed to advertise, but the counsellor (or gynaecologist)  can probably tell you the ones in your area.
4. The procedure just takes 1 - 2 hours. Complications are rare, other than a few days of unwellness. The fee (€400-500) has to be paid in advance by you.
5. Go to the clinic with your girlfriend and give as much emotional support as possible. Take a taxi back, as she will hardly be in the shape to walk or take public transport. She needs a few days rest after this.

Altho the above posts are almost a year old, I can only say "how sad".
Yes, I am against abortion at almost all cost.  My German girlfriend just
got pregnant in Sept. and in Oct. had a miscarriage.  Our pregnancy was
not planned, nor was it a "mistake".  We just let nature take its course
for us. We were thrilled, then of course devastated. So sad, that in so many
cases with younger generations, it's "easy come, easy go", all in the name
of a career.  End of my soap box.