The German champions registered a 6-1 win to book their place in the semi-finals with a 7-4 aggregate result, but the Spanish coach could now be hit with a fine.
Proceedings are thought to centre on a T-shirt worn by Guardiola at his pre-match news conference - emblazoned with the slogan '#JusticiaParaTopo', or Justice for Topo.
The T-shirt was a reference to Argentinian reporter Jorge 'Topo' Lopez, who died in a car crash during last year's World Cup in Brazil.
UEFA confirmed on Wednesday that Guardiola had been charged with an alleged breach of article 11 (2) (c) in their disciplinary regulations - which concerns using "sporting events for manifestations of a non-sporting nature".
Porto boss Julian Lopetegui also faces action after being sent from the touchline on Tuesday.
