Jody Morris's youngsters had too much for Manchester City over two legs and recorded an emphatic 6-2 aggregate victory at Stamford Bridge.
The west Londoners have now lifted the trophy in each of the last four seasons, which is testament to the talent - and coaches - within the club's youth Academy.
Conte attended the game alongside Chelsea owner Roman Abramovich and was among the first people to visit the home dressing room to offer his congratulations to the players, all of whom have aspirations to force their way into the Italian's first-team fold.
"Congratulations - it was a really good game," Conte told the club's victorious youngsters.
"I think you deserved to win the trophy. It's very important to win for us this competition with a big tradition.
"I'm pleased for you and I hope you're going to continue in this way and continue to improve."
The Italian coach added "well done" before leading a round of applause in appreciation of the players' achievement.
Antonio Conte was one of the first to congratulate our Under-18s after the game...👏 pic.twitter.com/StNu27gx1P— Chelsea FC (@ChelseaFC) April 27, 2017
Conte has given more opportunities to youth since taking charge at Chelsea, with Ruben Loftus-Cheek, Nathaniel Chalobah, Nathan Ake and Ola Aina all afforded game time this season.
The Blues boss has spoken of his desire to see more youngsters reach the first-team on several occasions and recently stated that even a 'squad role' should be viewed as a fantastic opportunity to progress.
Meanwhile, Chelsea are on course to win their fifth Premier League title this season.
Conte's side are four points clear of Tottenham with five games left to play and travel to Everton this weekend aiming to take another step towards silverware.