The pharmacist admitted failing to read the prescription correctly in February 2012 when she mixed the eye drops.
It left one baby partially sighted in both eyes, while two others lost the sight in one eye. All were being treated at a clinic in Wuppertal, North Rhine-Westphalia, where the woman worked.
A doctor and a second pharmacist who were involved in the error have already agreed to pay €7,000 and €6,000 respectively.
By agreeing to pay a fine of €6,000, the 52-year-old woman avoided being charged with bodily harm resulting from negligence.
The case would have started on Wednesday if the woman, from near Cologne in North Rhine-Westphalia, had she refused to settle.