The result means the All Blacks climb back above Wales to top of the world rankings despite the weekend's record defeat to the Wallabies.
An England line-up featuring only a handful of regular first-choice starters overpowered Wales thanks to tries from Billy Vunipola, Joe Cokanasiga and Luke Cowan-Dickie, as well as flawless kicking from captain and flyhalf George Ford.
The visiting Grand Slam winners struggled for attacking cohesion throughout, despite tries for Gareth Davies, George North and Alun Wyn Jones, and compounded their woes with an injury to first five Gareth Anscombe.
Wales have not won at Twickenham since the last World Cup and never looked like ending that run to spoil the occasion of skipper Alun Wyn Jones becoming his nation's most capped player.
Wales captain Jones told Sky TV: "We probably came out of the blocks a bit slow. You're always wary of that first 20 minutes, whether international or domestic. We feel we probably let in two soft ones.
"We're professionals. You can't say you're rusty coming off the break. We're well aware where we let ourselves down in that first half.
"We've got another opportunity next week. This is the first one on the journey this season and obviously there's going to be lots to work on."
Debutant half back Willi Heinz was among a number of fringe England players that advanced their claims for inclusion in the World Cup squad that Australian coach Eddie Jones will name.
And man-of-the match Vunipola said: "Today was the perfect example of a game that could have gone away from us. We stayed in the fight and we managed to come out with the win, but you can never read too much into these pre-season games, these warm-up games.
"I know everyone's been calling them 'Tests', and they are Tests, but Wales under that pressure probably perform to their peak level.
"We played well in patches, but there's still room for improvement."
England play three more warm-up matches - away to Wales and at home against Ireland and Italy - before heading to Japan, where they kick off their campaign against Pool C opponents Tonga on September 22.
England's only concerns from this morning's game will be the fitness of flanker Tom Curry, who impressed before limping off early, and their habit of conceding clusters of penalties.
Wales, meanwhile, will need to regroup ahead of the return fixture in Cardiff on Saturday, and work out how a defence that only conceded seven tries in the whole Six Nations and rarely left gaps was pierced so regularly by England.
Wales mentor Warren Gatland promised Wales would up their game next weekend.
"England went back to traditionally what they're good at," the New Zealander said.
"The scrum was good, the driven line-out was good. They played it fairly tightly but we'll have a look at our approach for next week.
"Any loss is disappointing, but this is not our competition face. There were a few too many turnovers. We will be a lot better next week."
The two sides could face each other in the World Cup quarter-finals in October.