Rooney, playing at No 10, then turned the match in the second half by equalising from closerange and converting a penalty after substitute Marcus Rashford had been fouled.
In this truer test, the hosts' long unbeaten league run on Merseyside never looked under real threat until late on, when Alisson made two vital saves to deny Bruno Fernandes and Paul Pogba from closerange.
Dani Carvajal fired in an excellent opener at the near post and Vinicius Jr chested in at closerange from Rodrygo's cross before the break. Vinicius then finished low into the corner after 49 minutes for his second.
Nketiah, leading the line in place of the injured Gabriel Jesus, converted the opener coolly from Declan Rice's cross in the first half then capitalised on a Wes Foderingham error to slam home a close-range second soon after the break.
But Arturo Vidal thumped in a shot and Thomas Muller guided in a close-range effort to put the Germans in front. Benfica drew level on the night through Talisca's curled free-kick, but a comeback was beyond them.
Barca were below par, falling behind to a close-range Joselu finish. Luis Suarez equalised seconds after the restart but an Alex Bergantinos header sealed Depor's win.
Fabregas hit the bar before Pedro's curling effort restored the lead and Diego Costa netted the third from closerange. Swansea were denied a penalty when Cesar Azpilicueta handled inside his area at 1-1.
Jose Mourinho's side were fortunate to emerge from a sloppy 25-minute opening spell only one goal behind after Callum Wilson deservedly fired the hosts in front from closerange.
Bryan Luiz volleyed Costa Rica ahead on 24 minutes, before Napoli striker Dries Mertens equalised from closerange. Lukaku scored either side of half-time and then set up Michy Batshuayi to tap home Belgium's fourth.