He has been charged with armed robbery and recklessly cause injury, and will appear at Melbourne Magistrates Court on Friday.
Another pharmacy employee, a 51-year-old woman from Taylors Lakes, was treated at the scene for a minor wound to her hand.
A second woman working at the pharmacy was not injured.
A customer, a 30-year-old man, who was in the store when the men stormed in, hid in the staff room behind the pharmacy and was unharmed.
Police are still looking for a second suspect.
Police have released CCTV images in the hopes someone recognises him.
He is perceived as African in appearance and about 181cm tall with a medium build.
He was wearing a grey hooded jacket, grey tracksuit pants with a thick stripe down the leg and distinctive red and white sneakers.
Anyone with information is urged to contact Crime Stoppers on 1800 333 000 or submit a confidential report online at www.crimestoppersvic.com.au.