Im sure they would have used perfectly safe and non reactive materials like lead, copper, silver, leather and sea sponges... Umm yeah good point.
They had glass, but I don't think glass tubes were perfected until the late medieval ages. Besides they didn't really do much microbe research until pasteur came along.
Pipettes didn't really happen until 19th Century I believe. So, for something like 150 years, this weird practice was used.