The move is designed to tackle the growing risk of drug-resistant bacteria like the so-called superbug, MRSA.
Health Minister Malcolm Chisholm said it was important the idea was woven into medical students' "working ethos" at the beginning of their careers.
MRSA has become a serious problem in hospitals.
It is a form of the staphylococcus bacterium that is resistant to the commonly used antibiotic methicillin.
The health minister said he believed that the overuse of antibiotics may allow superbugs to develop.
In recent years medical experts have warned that the unnecessary use of antibiotics permits the development of infections that cannot be treated easily.
Medical opinion
Announcing the new approach to dealing with all types of patient complaint, Mr Chisholm said it was vital medical students and GPs made the right choices.
He said: "Excessive use of antibiotics allows the development of drug-resistant bacteria."
"This not only makes infections more difficult to treat, but may increase the length and severity of illness and the length of hospital admissions.
"It also means that use of the limited numbers of antibiotics available become less flexible because of patients who have built up resistance to certain bacteria."
It was important to dispel the notion that antibiotics were the a cure for everything, the minister added.
"The public must remember that they do not cure common viral infections such as colds and flu and indeed have little or no effect on the course of such illnesses."
The initiative will see £100,000 being spent in Scotland's medical schools to train students to identify problems and use their knowledge effectively.
Antibiotics are used to treat a variety of illnesses such as TB, pneumonia, septicaemia, cellulitis and bacterial meningitis.
Professor Peter Davey, an expert in clinical pharmacology based at Ninewells Hospital in Dundee, said it was important to reduce inappropriate prescriptions.