Halfpenny had scored all of Wales' points during the match, sending each of his six penalties between the posts, but he was outshone by Lions fly-half Owen Farrell, who managed 19 points from the tee.
And the disappointment of Wales' defeat was compounded after the final whistle, when head coach Warren Gatland confirmed the injury.
"Leigh has dislocated his shoulder," said the New Zealander. "That's his season over."
Wales will face Scotland next weekend without their talismanic full-back, but Gatland's side still boasts a handful of Lions, including captain Sam Warburton and another star of the Australia tour, George North.
And the coach, who himself led the Lions last summer, is hoping to see a positive reaction from the players.
"I don't think there's a massive amount between these sides," he added.
"We got in at 20-15 at half-time having not played too well and we thought that if we were more accurate, didn't turn the ball over as much, then it could have been a pretty different ball game.
"A good performance against Scotland is paramount for us. At times we've played well and at times we haven't and that's disappointing so next week is vital."