For Aguero, it was a second miss of the week, after he failed to convert a penalty for Argentina during a 1-0 World Cup qualifying defeat at home to Paraguay on Tuesday.
Guardiola, though, insists he has bigger priorities than penalty practice as he attempts to get his team back to form.
Asked if his players had practised penalties, he said: "No. I don't have time to practise everything I want to practise.
"You can practise penalties in training, but in training, no one (a crowd) is there.
"In the final of the Champions League, that is crucial. If the player says, 'I want to be there' (take the penalty), that is enough."
Guardiola made a superb start to his reign as Manchester City manager, winning his first 10 matches in charge.
However, his players have gone three games without a victory in all competitions, and face a daunting Champions League trip to his former club Barcelona on Wednesday.
Guardiola said it was his responsibility to try and restore confidence to his players if that was an issue.
"I am here to try to make that happen.
"I try to analyse the reasons we don't win. Of course, the confidence and mood is much better when you win."
Despite the failure to beat Everton, City enjoyed 72 per cent of the possession and had 19 shots at goal to the visitors’ three.
"I am not frustrated with the team. I am sad for the players. They deserve to win the game. They did absolutely everything to win it," said Guardiola.
"Football is sometimes beautiful. They have to be more open, play a little bit more and find spaces."
Everton manager Ronald Koeman suggested Stekelenburg had the best game of his career after not only saving two penalties, but also making a world-class stop to deny De Bruyne later in the game.
"Maybe the goalkeeper played his best game ever. We know he is a very good goalkeeper," Koeman said of his fellow Dutchman.
"He saved two penalties and two more shots from Kevin De Bruyne.
"Maybe you need luck to get a result but I think we get a result today because the fighting spirit was amazing."
Koeman also indicated City are the best team he has faced in a managerial career spanning 15 years.
"It is the best team we have played against in my managerial career -– they have a really high tempo," Koeman said.
"We made some mistakes because the pressing was so high. I'm pleased with the point. We didn’t deserve more, I know.
"Maybe we didn’t deserve one, counting the number of chances, and the fact that there were two penalties missed but football is unpredictable and the key to get a point was the belief and the work rate of the players."