c. 1300, pardoun, "papal indulgence, forgiveness of sins or wrongdoing," from Old French pardon, from pardoner "to grant; forgive" (11c., Modern French pardonner), "to grant, forgive," and directly from Medieval Latin perdonum, from Vulgar Latin *perdonare "to give wholeheartedly, to remit," from Latin per "through, thoroughly" (from PIE root *per- (1) "forward," hence "through") + donare "give as a gift," from donum "gift," from PIE *donum "gift," from root *do- "to give."
Meaning "a passing over of an offense without punishment" is from c. 1300, also in the strictly ecclesiastical sense; the sense of "pardon for a civil or criminal offense; release from penalty or obligation" is from late 14c., earlier in Anglo-French. Weaker sense of "excuse for a minor fault" is attested from 1540s. To beg (one's) pardon "ask forgiveness" is by 1640s.
Strictly, pardon expresses the act of an official or a superior, remitting all or the remainder of the punishment that belongs to an offense: as, the queen or the governor pardons a convict before the expiration of his sentence. Forgive refers especially to the feelings; it means that one not only resolves to overlook the offense and reestablishes amicable relations with the offender, but gives up all ill feeling against him. [Century Dictionary]