The previously winless Tahs scored five tries to two on Friday night at Parramatta's Bankwest Stadium to notch their first victory in six matches and also a first triumph in their past six clashes with the Lions.
The home team made their supporters sweat, however, missing six out of eight shots at goal.
But a 76th-minute try to replacement prop Tetera Faulkner sealed the win after skipper Rob Simmons had left the field with an ankle injury.
Coach Rob Penney was pleased with a lot of elements of the Tahs' performance, especially their defence, after conceding 14 tries in their first three games.
"We've been very leaky on that side, we were a massive improvement tonight," Penney said.
Simmons was forced off early, but was hopeful he had only rolled an ankle.
Halfback Jake Gordon suffered hamstring tightness and like Simmons will undergo a scan.
Slick handling and astute running lines were a feature of the home team's much- improved performance after a 0-3 start to their campaign.
Prop Angus Bell, fellow rookie and five-eighth Will Harrison and debutant James Ramm all added youthful zest and purpose while the ubiquitous Hooper was involved in several of the tries.
"I'm just so pleased for the playing group that they managed to bring into the arena a lot of the stuff that we've been working on," Penney said.
"Just so proud of the leadership group that have taken a lot of responsibility over the last ten days."
Both teams were down to 14 men at stages in the first half.
Lions lock Ruben Schoeman was given a yellow card after punching Simmons.
Tahs flanker Lachlan Swinton was given a stint in the bin after a late no-arms tackle on Lions five-eighth Elton Jantjies.
Bell crossed for his first senior try in the fourth minute with a dynamic run to the line after Hooper offloaded in the tackle.
A strong run from the young prop while Schoeman was in the bin led to a fine cut-out pass from Hooper to hooker Robbie Abel who sent Swinton clear.
Jantjes put the Lions on the board with a penalty but the Waratahs were soon rewarded again for their enterprising play.
Hunt and winger Jack Maddocks combined to set up a five- pointer for No.8 Jack Dempsey.
Six minutes later, Swinton was binned and it was the Lions' turn to capitalise on a numerical advantage.
Flanker Marnus Schoeman crashed over from a driving maul from a lineout after the penalty awarded for Swinton's indiscretion.
Up 19-10 at halftime, the Tahs pulled 15 points ahead with a try to replacement outside back Ramm after a turnover forced by Hooper and featuring some fine touches from Harrison and Kurtley Beale.
Marnus Schoeman strolled over for a second five-pointer to give the Lions a sniff, as they pulled back to within seven points, before Faulkner's try settled the game.