The 40-year-old tactician believes that Atletico are more organised under Gregorio Manzano and admits that he was "very scared" after hearing about the long-term injury to Afellay
Atletico currently sit eighth in La Liga, and though they got off to a slow start in the competition, they go into this coming game on the back of two convincing 4-0 victories against Racing Santander and Sporting Gijon.
The Vicente Calderon outfit finished seventh in the league last season, 38 points adrift of Barcelona, which saw coach Quique Flores part company with the club at the end of the campaign.
Guardiola believes Atletico have registered significant improvements under their new coach, telling reporters at a press conference: "This season's Atletico play in a different way.
"The team have Manzano written all over it. They play very well and keep being very organised, just like they were under Quique Flores, but they play more through the middle.
"They have scored many goals and conceded just one, while creating many chances. I did not expect them to be doing this well and to have made such good signings."
The Catalan club have received good news from the treatment table, as Gerard Pique has been deemed fully fit for the encounter, but Guardiola refused to reveal whether he will return to his traditional 4-3-3 system.
"If I deploy three defenders, it is to attack better, to create more spaces, not to defend," he noted.
"I reviewed the game against Valencia today and if our opponents do things well is because they are good, not necessarily because we made mistakes."
The 40-year-old coach also stressed that Ibrahim Afellay's serious knee injury was a hard pill for him to swallow as the Dutchman is facing a lengthy spell on the sidelines.
"It is a shock, I was very scared," Guardiola said. "He is a sensitive kid and this is the first time he gets an injury like this. But six months go by very fast. We have not talked about signing a replacement for him."