The Brazilian is a star performer for the Ukrainian outfit but has been ruled out for Manchester City's visit on October 23, with Group F delicately poised after the first two rounds.
The 30-year-old Taison caught the eye playing against City in the competition last season but suffered knee ligament damage following a horror tackle from Igor Kharatin in Shakhtar's 1-1 draw with Zorya on Sunday.
City are just one point ahead of Shakhtar in a tight group, with serious doubts also Taison will make the return game at the Etihad in mid-November.
Taison was instrumental in Shakhtar's 2-1 victory over the Citizens last December, with reports Guardiola was even readying a bid for the samba playmaker then.
City lost the opening group game this term at home to Lyon but got back on track with a win at Hoffenheim, so the absence of Taison can only improve the chances of Guardiola's men still qualifying with the minimum of fuss