The Portuguese champion wasted little time stamping its authority on the game, with De Tomas, a recent signing from Real Madrid, netting his first goal for the club after four minutes.
Chivas responded well to that early setback and twice hit the crossbar in the early stages of the second half, also striking the post in the closing stages.
Bruno Lage's side took full advantage of those reprieves, with Rafa and Seferovic producing clinical finishes in the final 20 minutes to earn an impressive win at Levi's Stadium in California.
Benfica started in ominous mood and forged ahead inside just four minutes. Caio burst into Chivas' penalty area after a surging run and coolly picked out the unmarked De Tomas, who had the simple task of tapping in from three yards.
Chivas was a team reborn at the start of the second period, with Miguel Ponce and Alexis Vega crashing long-range efforts against the crossbar.
Raul Gudino produced a stunning reflex save to keep out Seferovic's thundering close-range header but there was little he could do about Benfica's second goal 20 minutes from time.
Jota threaded a precise pass into the path of fellow substitute Rafa, who showed wonderful composure to clip past the Chivas goalkeeper.
Seferovic was equally calm in front of goal three minutes later, latching onto Adel Taarabt's incisive pass and slotting past the onrushing Gudino to complete a routine victory.
There was more frustration for Chivas in stoppage-time when they hit the woodwork for a third time, this time the post denying Ponce's free-kick.