Sevilla had begun their campaign last weekend with a disappointing 2-1 home defeat to Valencia and finished 12th in La Liga last season.
But the Europa League winners should have picked up another European trophy in Athens.
Youssef En-Nesyri's header powered the Spaniards into a first-half lead, but the Moroccan was guilty of missing two huge chances when one-on-one with Ederson after the break.
City badly missed the creativity of Kevin De Bruyne and Bernardo Silva, who were sidelined by injury and illness respectively.
De Bruyne's four-month absence due to a serious hamstring injury has exacerbated the loss of goals from midfield caused by the departures of Ilkay Gundogan and Riyad Mahrez since the end of last season.
Mahrez's exit to Saudi Arabia has opened the door for Cole Palmer to make his impact on the first team.
The England Under-21 international won man of the match after his headed equaliser rounded off a fine individual display.
Yet, Guardiola was far from convinced after the match that even Palmer would be part of his squad once the transfer market closes on September 1.
He has been linked with a move to West Ham as a makeweight in City's pursuit of Brazilian international Lucas Paqueta.
"I don't know (if he will stay)," said the City boss. "When we arrived (to Athens), I had the opinion that he wanted to leave but now I don't know.
"I don't think a loan is going to happen. He's going to stay or he's going to be sold."
Gruelling schedule
Under the baking heat in the Greek capital, Guardiola made only one substitution when Julian Alvarez was introduced late on for Palmer.
On top of defending the Premier League, Champions League and FA Cup, City are involved in the League Cup and are targeting the club's first-ever Club World Cup in December.
Guardiola has bemoaned his side's lack of preparation time for the new season and blamed a spate of major injuries across the top European leagues so early in the season on a gruelling schedule.
Real Madrid duo Thibaut Courtois and Eder Militao's seasons could already be over after suffering anterior cruciate ligament injuries.
Arsenal's new £40 million defender Jurrien Timber and Aston Villa's Tyrone Mings and Emi Buendia have also suffered similar injuries.
Chelsea's Christopher Nkunku had to undergo knee surgery on an injury picked up on a poor pitch during a pre-season friendly in Chicago.
"Look at all the cruciate ligament injuries there have been in all the big leagues this start of the season. The players don't rest either physically or mentally," said Guardiola ahead of the Super Cup final.
"They make them travel to Asia or America (on pre-season tours) for the club's purposes and play really hard games on bad pitches and the players get injured, or will get injured, because they don't have these 25 days to prepare."
Guardiola has always preferred to work with a small squad to enhance team spirit and cohesion.
City are aiming to become the first side to ever win four consecutive English top-flight tiles.
However, without further additions, they may be spread too thin in the coming months, offering hope to the chasing pack in the Premier League.
