Coach Warren Gatland had said this was not a shadow test team but few would complain if the same line-up, particularly the backline, were to run out to face the Wallabies in Brisbane in the first match of the three-game series next weekend.
Halfpenny scored two tries in four minutes around halftime and converted eight kicks from eight attempts to add 20 points in another flawless display with the boot at the Sydney Football Stadium.
The other scores came from flyhalf Jonny Sexton, flanker Tom Croft and the outstanding Jonathan Davies but there was bad news for the other Welsh centre Jamie Roberts, who will have scans on suspected torn hamstring and must be doubtful for the first test.
"It was a good effort and we're very pleased about the outcome," Gatland told a news conference.
"To be fair the Waratahs took it to us but I think the boys handled it magnificently (and) in the end we were just too big and too powerful for them."
The Waratahs, without 11 Wallabies through national duty or injury, gave the Lions only their second real contest of the tour in front of 40,805 fans and two tries from combative centre Tom Carter kept them in the match for the first 50 minutes.
Winger Simon Zebo, called up as cover for Tommy Bowe, had an excellent game and nearly made a spectacular start to his Lions debut after 38 seconds when he finished off a blindside move, only for the TV pictures to show that his left boot had grazed the touchline.
After Halfpenny had opened the scoring with a penalty from halfway, Zebo was involved in another move down the same flank, releasing Davies whose fine pass found flyhalf Sexton in support and the Irishman finished with a flourish.
Halfpenny converted to make it 10-0 after eight minutes but the Waratahs were not going to be blown away and it was their combative centre Tom Carter who got on the scoresheet next.
Bernard Foley's crosskick from inside his own half found Peter Betham charging down the left wing and he tossed the ball out of the tackle to Carter who, despite his evident lack of pace, got to the line before the cover defence.
Halfpenny extended the lead to 13-7 with his second penalty but the Waratahs stormed back and huge lock Will Skelton stormed over the line after a well-worked line-out but lost the ball in the tackle of Mike Phillips.
Brendan McKibbin and Halfpenny traded penalties but the Lions fullback had the last word in the opening half when he ran in for his first try on an overlap and converted to send the tourists into the break 23-10 up.
Halfpenny's second try came four minutes after the break after a neat midfield move had set Davies free and the centre's pass sent his fellow Welshman scuttling over the line.
The Waratahs were not about to fold, however, and Carter crashed over the line from close range after more good work from Skelton for a converted try to cut the deficit to 30-17.
Another Halfpenny penalty extended the lead and flanker Croft just about assured the victory with his try after a Davies interception on 55 minutes, fending off centre Tom Kingston on a powerful run to the line.
Six Lions replacements just after the hour mark disrupted the tourists' rhythm but Davies got reward for a fine performance when a Ben Youngs pass left him with a free run to the line.
Waratahs centre Rob Horne's chances of playing in the first test, already thin after being released from the Wallabies squad to beef up the home side, could disappear if he is cited for an early tip tackle on Halfpenny.
"We were able to put some good moves together ourselves but perhaps lacked a bit of the X factor to finish it off," said Waratahs coach Michael Cheika. "Probably on turnover ball their class really showed."
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