A drop goal from fullback Zarn Sullivan a minute after fulltime secured the Blues a record 13th consecutive victory and consigned the Waratahs to sixth spot on the ladder.
The defeat leaves the Waratahs needing to travel to New Zealand for a knockout quarter-final against the Chiefs next Saturday.
They had been hoping to play the Brumbies much closer to home in Canberra.
"It's a disappointing finish for us at Leichhardt Oval," said Waratahs captain Jake Gordon.
"We thought we started that second half really well and put some pressure on the Blues but we weren't clinical in the last 20 minutes."
Already assured of top spot ahead of the finals, the Blues rested all but one of their starters from last week's equally thrilling win over the Brumbies.
But even without superstars like All Blacks playmaker Beauden Barrett, impressive league convert Roger Tuivasa-Scheck and skipper Dalton Papalii, the Blues still had enough strike power to deny the Tahs a third Kiwi scalp in a single season for the first time in seven years.
The Blues kept the Waratahs scoreless in the first half even while reduced to 13 players after back-rowers Akira Ioane and Adrian Choat were both shown yellow cards in the space of a minute.
The visitors, in fact, posted the only points of the half while two men short, Jock McKenzie's penalty goal three minutes before the break giving the Blues a 3-0 lead.
Two tries in six minutes from winger Mark Nawaqanitawase midway through the second half shot the Waratahs out to a 14-3 lead.
Replies from replacement Cameron Suafoa and lock Luke Romano put the Blues back in front before a 78th-minute penalty goal from Tahs five-eighth Tane Edmed locked the game up.
But Sullivan had the final say as the Blues clinched a quarter-final date in Auckland next week with either the Highlanders or Western Force.
While the Waratahs were disappointed, their return to the finals in 2022 comes after their depressing winless campaign last year.
"It's been a massive improvement for us," Gordon said.
"We are happy with that but we are not getting ahead of ourselves. We've got a tough test next week."