The visitors took the lead with a touch of fortune and a sense of deja vu in the 25th minute.
It was not quite a carbon copy of Fernando Torres' late winner against Manchester City on Sunday but it was certainly close as a high, looping ball caused confusion in the Arsenal defence and the unlikely figure of Cesar Azpilicueta (above) ran through to get a toe on Carl Jenkinson's poor header towards Lukasz Fabianski.
There was nothing lucky about the second, however, as Juan Mata showed some fine skill, controlling with his left before lashing home a right-footed shot.
Manchester United will join Chelsea in the last eight after dispatching Norwich City 4-0 with Javier Hernandez scoring twice.
He got his first from the spot in the 20th minute after Leroy Fer felled Adnan Januzaj, and then headed in a second on the rebound just after the break.
Phil Jones volleyed in a third but by then, Norwich were more concerned about the condition of the Scotland striker Robert Snodgrass, taken off on a stretcher wearing a neckbrace, after a lengthy stoppage which followed a nasty clash of heads.
The incident led to 11 minutes of added time being played, and United used them to add a fourth through substitute Fabio.
Chris Hughton, the Norwich manager, later confirmed that Snodgrass was knocked out during the incident.
"He got a knock to his eye socket and he got concussion. He's been taken to hospital as a precaution," said Hughton.
Fulham's patchy league form carried over into the cup as they were knocked out by Leicester in a 4-3 thriller at the King Power Stadium. Elsewhere, West Ham edged out Championship leaders Burnley 2-0 at Turf Moor with both goals coming from the spot.