Kompany has been sidelined since injuring his calf on international duty with Belgium earlier this month, while Gundogan is suffering from a knee problem sustained in the Carabao Cup win over West Brom last week.
Both players are back on the training pitch but the game against the Ukrainian champions has come too soon for them to be involved.
However, Guardiola says left-back Benjamin Mendy faces a late fitness test before a decision is taken on whether he will play after the Frenchman was withdrawn early during Saturday’s 5-0 win over Crystal Palace.
“Vincent is not ready for tomorrow,” he said. “Ilkay trained yesterday part of the training. Vincent is similar.
“We are going to make a test if he [Mendy] is able to play.
City go into the game in fine form, unbeaten in their first eight matches of the season having scored 27 goals in all competitions.
Their 5-0 win over Crystal Palace on Saturday means they are the first side since Blackburn Rovers in 1958-59 to score 5+ goals in three consecutive top-flight matches in the same season, and they sit top of the Premier League table on goal difference from Manchester United.
But Guardiola is refusing to allow complacency to set in and says there’s always room for a side to improve.
Benjamin Mendy is back in Manchester City’s squad for Wednesday’s Champions League match against Shakhtar Donetsk. The defender has not played since April due to ongoing knee problems.
The Frenchman has been building up his fitness over the past few weeks, and manager Pep Guardiola has said he was hopeful that the player would return to first team action “in the next few games.”
Mendy’s return to the squad means the Citizens have just three players on the treatment table; two of which are long-term. Phil Foden is not in the travelling party to Ukraine with City stating that the midfielder is not fully fit.
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Aymeric Laporte is out for up to six months after sustaining a serious knee injury in the 4-0 win against Brighton earlier this month. The French defender is expected to be back to full fitness before the end of February.
Leroy Sane is estimated to be out for a similar length of time with his ACL injury. Fans will be hoping for a speedy recovery as both are key players for Pep Guardiola’s side.