Jenkins in for injured Lydiate
Lydiate, who captained Wales in the 27-13 loss in the absence of Sam Warburton, looked distraught as he went off halfway through the first half.
The Welsh Rugby Union released a statement saying uncapped Cardiff Blues flank Ellis Jenkins had been called up as a replacement.
"Ellis Jenkins has been called into Wales' squad to tour New Zealand after injury to Dan Lydiate," said the statement.
"Lydiate, who led Wales against England at Twickenham this afternoon, has suffered a shoulder injury, which he will fail to recover from in time for the three-Test series."
Speaking before the WRU statement, Wales coach Warren Gatland admitted Lydiate had little chance of making the flight to New Zealand on Monday.
"He is struggling. He has got a hamstring and potentially an AC [shoulder] injury as well," said Gatland of the 57 times-capped Ospreys flank, adding that he would need a "miracle" to recover in time.
"I think Dan has got to process it himself in terms of the tour could already be over for him. It is incredibly
"He will go back to the hotel to have ice and stuff. The assessment from our physios doesn't look very positive at the moment."
Wales were already without wing Alex Cuthbert and flank Justin Tipuric through injuries for the New Zealand trip, while Warburton is recovering from a shoulder injury that sidelined him this weekend.
Warburton, though, is expected to be fit for the opening Test against New Zealand in Auckland on June 11. And Warburton insisted: "I can't wait for the Tests in New Zealand. We will be going there to give it everything we have, and we are confident we can compete with them even though they are not world champions for nothing."
Agence France-Presse