Juve already had top spot in Group D wrapped up ahead of their trip to Leverkusen, who needed to avoid defeat to have any chance of advancing to the last 16.
Peter Bosz's side had the best of the chances in the first half but Ronaldo tapped home from Paulo Dybala's cross in the 75th minute and Higuain drilled into the bottom-right corner in stoppage time to send the hosts into the Europa League.
Buffon praised Ronaldo and Higuain for showing their team-mates they must work hard in every match throughout the season.
"If we face the games this way, I am sure we can all do great things. However, if we approach matches with a sense of snobbery, that becomes a problem," Buffon told Sky Sport Italia.
"It's a bad sign if you don't go into games with the right determination if you are 20, let alone in your 40s.
"I am glad that we had examples like Higuain and Ronaldo to lead the way in their performance, work ethic and show of sacrifice for the team."
"I want to take this chance to congratulate Napoli and above all Atalanta, because seeing what they are achieving is honestly emotional," Buffon added.
"I messaged [coach Gian Piero] Gasperini after the first couple of games and told him to believe, because they are the kind of team who can beat anyone. They can lose to anyone, but on their day, they can beat anyone.
"I am so happy they qualified and it's a wonderful story."