The Blaugrana were staring at a defeat after Alvaro Negredo double the Andulusians' lead in the second half after Piotr Trochowski had opened the scoring before the break.
Fabregas and Villa had the last laugh, however, with the midfielder bagging a brace before the striker sealed the three points with an injury-time winner.
"Villa is absolutely vital," the 43-year-old lauded to reporters after the match. "He has an important knack for scoring these types of goals."
"It was the reason behind my idea to deploy him as centre-forward. After just a month of being back in action, it couldn't have gone any better for him. The 3-4-3 formation has proven vital in helping Villa leave his mark.
|VILLA STRIKES AGAIN|
|5/1||David Villa is 5/1 with William Hill to score two or more against Benfica|
"This is a very strong league, and it is always better to have an advantage over Real Madrid than not to have it. Still, there are many games left, and many pitfalls await us, and them, over their course."