As well as Messi, World Cup winners and first-team regulars Xavi Hernandez, Gerard Pique, Andres Iniesta, David Villa, Carles Puyol and Victor Valdes are all being rested ahead of next Saturday's clash at Wembley.
The news comes as Sir Alex Ferguson hinted that he would start with a strong side side against relegation-threatened Blackpool at Old Trafford on Saturday.
Rested: Lionel Messi has 52 goals in 54 games this season
'I have players who need a game,' said Ferguson. 'Darren Fletcher, Paul Scholes, Anderson, Dimitar Berbatov, Patrice Evra and Edwin van der Sar will play.'
With the La Liga title clinched with two games to spare, coach Pep Guardiola has taken the opportunity to rest his key men before they travel to London to try and win back the trophy in a repeat of the 2009 final - which they won.
Fitness battle: Darren Fletcher is hoping a good performance on Sunday will force him into contention for a Wembley place
Although they are the favourites for the final, Barca's squad is much smaller than United's with the likes of Messi having played over 50 games this season.
And their last game against Malaga is effectively a dead-rubber with the south coast side having already secured their safety for another season.
Those first team regulars not rested for the Malaga match are Dani Alves, Sergio Busquets, Javier Mascherano, Eric Abidal and Pedro.
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Explore more:People: Alex Ferguson, Paul Scholes, Darren Fletcher, David Villa, Gerard Pique, Victor Valdes, Dimitar Berbatov, Patrice Evra, Javier Mascherano, Pep Guardiola, Edwin Van Der Sar, Lionel Messi Places: Barcelona, London