Arteta left his role as assistant at City last December to take charge at the Gunners, and while it has been far from straightforward for the Spaniard since, he could be on course to finish a topsy-turvy campaign with silverware.
Aubameyang was the hero as he struck twice at an eerily empty Wembley, sending his side through to face Chelsea or Manchester United on 2 August (AEST).
City huffed and puffed throughout but was unable to blow Arsenal's well-constructed house down, suffering its first defeat at the national stadium since going out to the Gunners at the same stage of the competition three years ago.
Guardiola fielded the same starting XI that won 3-0 when these teams returned to Premier League action in June, when the master easily overcame his former apprentice in Manchester.
However, the cup holder never hit the same heights in familiar surroundings in the capital, failing to respond after Aubameyang converted Nicolas Pepe's cross with a half-volleyed finish in the 19th minute.
The Gabon forward had missed a glorious chance earlier in proceedings, shooting straight at Ederson when clean through, but made no mistake when stretching out to poke the in-swinging right-wing cross back across the face of the Brazilian goalkeeper and in via the far post.
Shkodran Mustafi saw a header tipped over in the closing stages of a first half that saw a rather sluggish City fail to muster a shot on target.
Raheem Sterling carelessly missed the target soon after the break, but Emiliano Martínez was finally called into action to keep out a low attempt by Riyad Mahrez, while the goalkeeper was grateful to see a Kevin De Bruyne free-kick ripple the outside of the net.
Aubameyang, however, had no such issues locating the goal during a rare Arsenal attack in the 71st minute, running onto Kieran Tierney's lofted pass before slotting through Ederson's legs.