How to read the traffic light at this German intersection?
You're meant to cross the crossing in two steps (you'll need two traffic light cycles to turn left, not like cars who manage in one cycle).

I took the road names from here, which is, I think, the crossing you were photographing.

Starting from Jahnstraße, you go straight (on the right of the lane) along with the cars coming from Jahnstraße. Arrive at the holding line I marked in red . (And see all the cars with the same destination as you, cruise off over the river while you wait). Now you're standing in front of the cars going along Berliner Straße facing south.

For the second step, the small traffic light you highlighted is relevant (and the way these crossings are meant to be used, from this position it should be visible, but they are commonly misadjusted, don't know why, but it seems they see less maintenance). It's purpose is to give you a small head start ahead of the traffic queueing up behind you in Berliner Straße. This is why it's so short green, it's only for the few people getting packed in this short term "parking spot", it is not meant to be caught by flowing traffic. In addition to the headstart, it's meant to tell you when Berliner Straße has green - there's no way you can see the main signal.

EDIT: as top view (image from google maps)


you arrive on the black line
wait until the green traffic light turns green
continue on the green line
wait until the red traffic light turns green
continue on the red line




EDIT: for the benefit of those who want to take another look at the concept: similar bike-left-turn solutions exist in other towns, here in geneva, with streetview

with two of these small wait-spaces to wait for green on the next leg:



EDIT (adding some points raised in the comments):

This way of turning left is typically a safe and easy way to turn left on crowded crossings, even if you're not very familiar with roads. The biggest danger is cars turning right and running over you when you go straight on the first leg - that's the same as when you go straight and unfortunately omnipresent in Germany, not only on crossings like these. If you're confident to do it, you can probably also turn left on the car lane - it might be a bit of a hazzle to reach that lane, I'm not sure how legally evil that is, but it's probably not too problematic if you know the crossing. I cannot judge how much of an obstacle you'll become for cars turning left - I think it's two lanes turning left in parallel.

In my experience you're meant to do the 90° turn before coming to a stop in Germany, and after the stop in Switzerland; such that in your case you just accelerate straight once the second traffic light turns green, that's the position for which the traffic light should be adjust.

PS: on the top view you can also see similar waiting places for coming from the south on Berliner Straße and turning left into Im Neuenheimer Feld; and with lane marking, the way to go from the north into Jahnstraße to the east.