GlaxoSmithKline argued there was nothing in its contract with the pharmacy that entitled the chemist to compensation, but Judge Wiltens found the written and oral contracts between the two parties implied proper payment for the services.
The contractual obligations did not deal with recall situations and the arrangements were "deficient in that regard", he said.
The need for a recall stemmed from GlaxoSmithKline, and the pharmacy's work was necessitated by the drug company's error.
Pharmacy Guild president Karen Crisp welcomed the judgment, saying it had successfully established a precedent that pharmacists could reasonably expect to be paid when asked to provide services.
The judge had clearly stated that an ethical or moral duty did not negate any right to be paid for the time and effort of doing the work, she said.
"This is an important principle affecting all people working in the heath system."