The Spanish midfielder is still nursing an injury and will not be able to take part in the first-leg of the last-16 tie in Russia
The Spanish midfielder missed Saturday's 4-1 victory against Nacional in the Portuguese Liga and Jesus confirmed after the game that the player will not recover in time for the match in Russia.
"Javi suffered an injury yesterday [Friday]," Jesus told reporters. "I am sure he will not go to St. Petersburg."
To replace Garcia in front of the defence, Jesus will deploy Nemanja Matic, who was a starter in Saturday's match.
"Matic had a great game, even though Javi is much more used to the team's movements than he is," Jesus added.
Benfica, who finished at the top of their Champions League group, take on Zenit at 18.00CET.