Dictionary.com
definitions

bene-

a combining form occurring in loanwords from Latin, where it meant “well”: benediction.

Origin of bene-

combining form of bene (adv.) well (< *dwenē), akin to bonus good (< *dwenos)
Dictionary.com Unabridged Based on the Random House Unabridged Dictionary, © Random House, Inc. 2019
Word Origin and History for bene-

Latin word-forming element meaning "well," from Latin bene "well, in the right way, honorably, properly," from PIE *dw-ene-, adverbial form of root *deu- "to do, perform, show favor, revere." Cf. Latin bonus "good," bellus "handsome, fine, pretty," beatus "blessed."

Online Etymology Dictionary, © 2010 Douglas Harper