late 15c., "with subtraction of," from Latin minus "less," neuter of minor "smaller," from PIE *mi-nu-, suffixed form of root root *mei- (2) "small."
According to OED, this mathematical prepositional use in expressions of calculation was not in the classical Latin word and probably is from North Sea medieval commercial usage of Latin plus and minus to indicate surplus or deficiency of weight or measure.
The origin and original signification of the "minus sign" is disputed. As "deprived of, not having," by 1813. Of temperature, etc., "below 0 or the lowest point of positive reckoning, belonging to the inverse or negative side," by 1811.