A dominant performance was rewarded by an early second-half strike from the German youngster and an all-English clash against the Blues now awaits in the last four
The German youngster struck early in the second half as the Gunners' NextGen side continued to provide a silver lining to the north London club's season with a dominant performance against the Russian outfit.
The hosts enjoyed numerous chances in an impressive showing but CSKA shot-stopper Sergey Revyakin produced a fine performance to keep the scoreline deceptively tight.
Terry Gibson made two changes from the hosts’ 1-0 win over holders Inter Milan, with Elton Monteiro and Zak Ansah making way for Thomas Eisfeld and Kyle Ebecilio.
The visitors, meanwhile, made just one alteration from their 3-0 win over PSV Eindhoven as coach Alexander Grishin brought David Khurtsidze in for Gela Zaseev.
A sense of anticipation greeted the players as they took to the field, with a boisterous Emirates Stadium crowd cheering every Arsenal move from the off.
The hosts fed off the intimidating atmosphere in the opening few minutes as Chuba Akpom first forced Revyakin into action, before Gnabry headed straight at the Russian after a fantastic cross from Hector Bellerin.
The visitors were next to threaten, however, as Konstantin Bazelyuk - who scored twice in the last round - forced a corner on nine minutes.
Comical defending then allowed left-back Pavel Kotov to break free and force another corner, but as the cross floated harmlessly into Deyan Iliev’s arms the early signs were that this clash was Arsenal’s for the taking.
Gnabry came close once more on the half-hour mark, latching onto a fine through-ball before trying to place a low shot past Revyakin only for the keeper to again thwart the home side and beat the ball away with a firm save.
It was a surprise that it took Arsenal so long to break the deadlock, Gnabry - who was sensational throughout - made a fine run into the box before playing a neat one-two inside the area and calmly gliding the ball past a helpless Revyakin early in the second half.
The 17-year-old was on hand to stop Akpom and Eisfeld minutes later, however, and but for his contribution – Arsenal could have increased their lead by several.
Next to be denied was Angha, who saw his shot smothered inside the area, before Akpom then came close and a free kick crashed against the bar late on.
But despite their unrelenting desire for a second, one goal would prove enough to see the Gunners through – and a scintillating all-English semi-final against Chelsea now awaits.