The punishments stemmed from post-match incidents following Fenerbahce's 2-1 victory in Lyon, where the two players were accused of making provocative gestures towards the home fans.
The confrontation escalated after the final whistle, with a brawl breaking out as Frenchman Guendouzi left the pitch.
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European football's governing body said Guendouzi was fined €50,000 ($58,060.00) "for insulting others present at the match, provoking spectators and violating the basic rules of decent conduct" and suspended for four UEFA club competition matches.
Englishman Greenwood was fined €30,000 and suspended for one match for violating the basic rules of decent conduct.
Two of Guendouzi's suspended four matches were deferred for a probationary period of one year, while Greenwood's one-match ban was subject to a one-year probationary period.
UEFA also sanctioned both clubs for crowd disturbances, the throwing of objects, lighting of pyrotechnics and violation of the rules of conduct at the match.
Lyon goalkeeper coach Antonio Ferreira was handed a five-match ban for "serious assault", with two of those matches suspended for a probationary period of one year.
Fenerbahce progressed to the league phase of the Champions League with a 3-2 aggregate victory.