The strike duo missed training on Monday to spark talk that they could miss Tuesday's crunch clash with Bayern in UEFA Champions League Group E.
But when asked about the absence of Aguero and Jovetic, City boss Pellegrini said in a press conference: "Both of them are in the squad list."
That will come as a huge relief to City fans with Edin Dzeko sidelined with a calf injury and teenager Jose Angel Pozo the only other striker in Pellegrini's squad.
The Premier League champions will also be without David Silva and Aleksandar Kolarov due to knee and calf injuries respectively, while Yaya Toure and Fernandinho are suspended for the crucial encounter with Pep Guardiola's men.
City's chances of progressing to the last 16 look slim as they sit bottom of Group E with only two points ahead of their final two matches against Bayern and Roma.
They must win or hope the clash between Roma and CSKA ends in a draw to have any chance of staying in the competition - and Pellegrini has not given up hope of securing second spot.
He added: "It is important for this club to do well in Europe. Tomorrow the team will fight to the end to continue in the Champions League.
"If we don't qualify we will analyse [why they failed to do so]. But we must play the game tomorrow and against Roma before drawing conclusions."
City were beaten by a late Jerome Boateng strike at the Allianz Arena in September, but Pellegrini is not dwelling on that defeat.
He said: "We were unlucky to lose in the last few minutes. But what happened in the past doesn't matter."
