1520s, "to pierce into or through," from Latin penetratus, past participle of penetrare "to put or get into, enter into; cause to go into." This is related to penitus "within, inmost, interior," penetralis "penetrating; innermost;" penus "innermost part of a temple, store of food," penarius "used for storing food;" Penates "household gods."
All are from penus/penoris "food, provisions," from Proto-Italic *penos, from PIE *penos "food" (source also of Lithuanian penėti "to feed"). De Vann writes that "The semantic appurtenance to 'feed' is explained by Stüber as 'what one feeds with' ('food') > 'the place one feeds at' > 'interior, home'."
The figurative senses of "enter and affect deeply, influence, impress" and "gain intellectual or spiritual access" are from 1580s. Related: Penetrated; penetrating.