Ramires fired the Blues into an 11th-minute lead after a Jay Spearing mistake allowed the Brazilian through, and Didier Drogba doubled their advantage with a close-range finish seven minutes after half-time.
Liverpool were spurred into life when substitute Andy Carroll smashed his effort into the roof of the net in the 64th minute.
And the Reds thought they had equalised soon after – but Carroll’s header was adjudged not to have crossed the line before Petr Cech clawed the ball clear.
Despite relentless late pressure from Kenny Dalglish’s men, the Londoners held on to secure their third FA Cup triumph in four years.
“I’m very happy for the players because we’ve been heavily criticised this season,” said Di Matteo, who won the cup twice with the Blues in 1997 and 2000. “We’ve got a trophy and we still have the chance for another one.
“It’s been a difficult season for us but this group of players have made the club proud today. It’s been hard work for us but in the end we came through.
“It’s quite a unique situation to be able to win the FA Cup as a player and then be able to coach the team and win it as well. I feel honoured to have been given this chance.
“I think we played well today. I think we deserved it. We scored two very good goals. They pressed us hard in the second half but I think we defended well again.
“We still have two Premier League games to play which could be vital for us and then we’ll focus on Munich.”
Chelsea midfielder Frank Lampard was full of praise for interim boss Di Matteo and the impact he has had at Stamford Bridge since taking over from André Villas-Boas in March.
“Until they scored it was very comfortable. It was hard to deal with but we deserved to win. Didier Drogba is my hero. No striker I’ve seen scores so many important goals in finals. Roberto deserves everything, he’s turned the club around.”
“It’s a massive day, the FA Cup final is huge to this club and an amazing feeling. We can certainly celebrate tonight, we’ll deal with the game on Tuesday [the Premier League game at Anfield] when it comes.”
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