Kompany has struggled with injuries in recent seasons while Aguero has often been linked with a return to Spain.
Neither player started in City's 4-0 defeat to Barcelona in the Champions League on Wednesday which has cast an element of doubt over both their futures.
Belgian international defender Kompany has struggled with injuries in recent seasons while Aguero has often been linked with a return to Spain's La Liga.
Guardiola dismissed out of hand the link between their absence from the starting line-up and being considered surplus to requirements.
"I am sorry, when Sergio decides to leave Manchester City, it will be his decision," said Guardiola.
"I appreciate him like a football player and appreciate like a man what he did here.
"The next time before you give your opinion and you decide he is not in my plans you can call me!
"I spoke with Sergio, we talked about that, he was so understanding and helped us a lot from the bench and in the last minutes if the game was close, the last 30/35 minutes and their central defenders were tired, I thought Sergio could help us a lot."
Guardiola, who proved ruthless on his arrival in sending unwanted players such as Samir Nasri and Wilfried Bony off on loan, said Kompany -- who missed Euro 2016 because of injury -- was once again not fit enough.
"Vincent was not perfectly fit. That is why we took a decision to pick Pablo Maffeo," said Guardiola.
"We appreciate him a lot. Normally Vincent Kompany would be on the bench. But he was not fit.
"With respect to Sergio Aguero, I said after the game it was a tactical decision.
"I wanted one midfield player more in the middle with Kevin de Bruyne, he has the qualities to hold behind the line, behind the back four and make the movements behind the full-backs.
"I think I took a decision and my plans (are) they have futures."
Kompany would appear the more vulnerable of the two players given the amount of time he has spent on the treatment table.
The 30-year-old has started just one match - a 2-1 win over Swansea City in the EFL Cup - this season and made just 14 appearances in the Premier League in the previous campaign.
But ahead of Sunday's Premier League clash with Southampton at the Etihad Stadium, Guardiola claimed he remains a big admirer of the City captain.
"I saw him when he is fit, he is a real central defender. I like him," said Guardiola.
"We try to take care of him.
"It was him, he went to the doctors and said 'I am not available to play'. I am going to explain always what is the truth with players.
"We lost 4-0 to Barcelona. You want a guilty? I am guilty. We win? I am a genius. We win 10 games? You say we are going to win four titles," added the 45-year-old Spaniard.