Messi, Puyol and Afellay in King's Cup squad
Argentina forward Messi is available after returning from an extended holiday and Spain defender Puyol has recovered more quickly than expected from a leg muscle injury picked up in a friendly between Catalunya and Honduras at the end of last month, the club said on their website.
The pair missed Sunday's 2-1 home La Liga win over Levante.
Netherlands midfielder Afellay, bought last month from PSV Eindhoven for 3 million euros, could make his debut for the 2009 Cup winners against Bilbao in what will be Guardiola's 150th match in charge.
The Basque club, who lost 4-1 to Barca in the 2009 final, held the league leaders to a 0-0 draw in last month's first leg at the Nou Camp.