Ferguson compared Saturday's loss to the famous 4-0 drubbing United received from Barcelona at the Nou Camp in 1994, a result which helped redefine his team's approach to European competitions.
"It's not going to be easy, but that's the challenge," Ferguson said. "You shouldn't be afraid of a challenge. The one thing we have shown is that we are consistent in Europe.
"This may be the kind of stepping stone that we had some years ago when we got beaten 4-0. We improved after that and we want to improve after tonight."
Barcelona's victory was their second triumph in the Champions League in three years - and their third in six seasons.
Guardiola appreciates Barca players
Ferguson admitted that Barcelona would be difficult to beat so long as their star players Messi, Andres Iniesta and Xavi Hernandez remained in their ranks.
"I think that great teams do go in cycles, and I think the cycle they're in at the moment makes them the best in Europe, there's no question of that," said the Scot.
"How long it lasts, whether they can replace that team at a certain point, who knows? But they certainly have the philosophy.
"It's always difficult to say whether you'll be able to replace players like Xavi and Iniesta at a certain point. Probably not. But they are enjoying the moment and they deserve to because they play football the right way."
United centre-back Rio Ferdinand echoed his manager's comments, adding: "They are a fantastic football team with great individuals, but more importantly, they are a great collective team.
"We've got to aim to get to that and that's something for next season and we will come back fighting again next year."
“Irresistible all evening, United couldn't get anywhere near him - 10 out of 10”
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