At the end of a week in which the focus has been on the sudden return to rugby league of their high-profile code-hopper Benji Marshall, the Blues outscored the Sydneysiders two tries to one.
But in a game that did not reach great heights, the Blues struggled throughout to hold the ascendency while the Waratahs had ample possession but suffered from multiple handling errors
It was the Blues' fourth win of the season, all of them at Eden Park, and ended a two-match losing streak after they were downed by the Hurricanes and Brumbies in recent weeks.
"The boys really know how to play well at home. We were at a bit of a low point after losing those two games but we had to win this one and we did," relieved captain Luke Braid said.
The win lifted the Blues ahead of the Highlanders in the New Zealand conference.
The Highlanders still have to play the competition-leading Coastal Sharks in South Africa this weekend.
The Waratahs, with five wins, remain second on the Australian ladder, one point ahead of the Western Force who play the Northern Bulls on Saturday.
The Waratahs produced the pressure in the first half but a succession of handling errors meant it was the Blues that produced the points, turning with an 8-3 lead.
A penalty to Simon Hickey was followed by a try to Lolagi Visinia, who won the ball for the Blues when he outleaped Michael Foley to field a high kick and then finished the move by fielding a long pass from Ma'a Nonu to score in the corner.
The only reward for the Waratahs in the first 40 minutes was a Foley penalty after missing two close flirtations with the line.
In the opening minute Adam Ashley-Cooper sliced through the Blues defence, only for Rob Horne to be tackled just short of the line.
Horne later dotted down by the posts only to be brought back 55 metres for a knock on.
The Blues stretched their lead to 18-3 early in the second half with a second Hickey penalty and a converted try to Francis Saili.
Jacques
Potgieter eventually scored for the Waratahs at the end of a sustained
build-up, with Foley adding the conversion and a second penalty to close
the gap to 18-13 before a third Hickey penalty sealed the outcome.
Scorers:
Tries: Lolagi Visinia, Francis Saili. Conversion: Simon Hickey. Penalties: Hickey (3).
Waratahs:
Try: Jacques Potgieter. Conversion: Bernard Foley. Penalties: Foley (2).
More to follow
Teams:
Blues
15 Charles Piutau, 14 Frank Halai, 13 Francis Saili, 12 Ma'a Nonu, 11 Lolagi Visinia, 10 Simon Hickey, 9 Bryn Hall, 8 Peter Saili, 7 Luke Braid, 6 Jerome Kaino, 5 Tom Donnelly, 4 Patrick Tuipulotu, 3 Charlie Faumuina, 2 Keven Mealamu (captain), 1 Tony Woodcock
Substitutes: 16 James Parsons, 17 Sam Prattley, 18 Angus Ta'avao, 19 Hayden Triggs, 20 Piri Weepu, 21 Steven Luatua, 22 Ihaia West, 23 Pita Ahki
Waratahs
15 Israel Folau, 14 Cam Crawford, 13 Adam Ashley-Cooper, 12 Kurtley Beale, 11 Rob Horne, 10 Bernard Foley, 9 Nick Phipps, 8 Dave Dennis (captain), 7 Michael Hooper, 6 Jacques Potgieter, 5 Kane Douglas, 4 Will Skelton, 3 Sekope Kepu, 2 Tatafu Polota Nau, 1 Benn Robinson
Substitutes (from): 16 Tolu Latu, 17 Jeremy Tilse, 18 Paddy Ryan, 19 Pat McCutcheon, 20 Wycliff Palu, 21 Brendan McKibbin, 22 Jono Lance, 23 Matt Carraro, 24 Stephen Hoiles