Teach him a leave it command.Keep them separate with gates and when they are together the Gsd should be under control on a leash so you can enforce the command.Being consistent and willing to do as many reps as it takes will get you there.Reward calmly for success,if you're too enthusiastic he might get excited again and want to chase
I agree with Dogma.
Can you describe the small dog's behavior before and after being chased? How old and what breed is the little one? Sometimes the small dog can give off signals that we don't notice. A look can be a trigger for the GSD to give chase. You also need to be vigilant about the little dog and make him/her obey as well. They are smart and take advantage when the GSD is limited in his ability to chase, kinda like a 'teacher.'s pet'.