Jordi Cuixart and Jordi Sanchez are currently behind bars in Spain as the fight for freedom continues in Catalunya.
A vote for independence on October 1 sparked controversial scenes, with the Spanish Constitutional Court having ruled the poll illegal.
Cuixart and Sanchez have been detained as figureheads of the separatist movement, with the pair being held without bail while they are investigated for sedition.
A protest on Tuesday saw thousands take to the streets of Barcelona to express their opposition to the actions of the Spanish courts.
Guardiola has now offered his support to that cause, telling reporters after a midweek fixture in Europe.
"This win is dedicated to them [Cuixart and Sanchez].
"We have shown in Catalonia that citizenship is bigger than any ideas. We hope they will be released soon."
Guardiola, as a Catalan native, has been a public supporter of the push for independence.
He has previously taken in productive spells as a player and manager at Barcelona and is one of the more high-profile figures to have joined the debate.
For now, though, he is based in England and overseeing the piecing together of what he hopes will be another hugely successful spell in the dugout.
City’s win over Napoli has stretched the club’s unbeaten start to the season and taken them on to 10 successive victories in all competitions .
They top the Premier League table and their Champions League group, with positive progress having also been made in the Carabao Cup.