The Crusaders secured back to back wins when they beat the Rebels 19-25 in Melbourne but had to rely on penalties for their second victory.
Both the Rebels and Crusaders scored one try each in front of a 13,942 strong crowd.
Given the number of All Blacks in the Crusaders team they are playing well below where they should be but will have a bye next week to sort out their problems.
Seven time champions the Crusaders usually have slow starts to the season but this year they appear to be struggling more than usual.
The Rebels travel to Sydney next week where they will face the current Australian conference leaders the Waratahs.
Centre Tom Taylor proved the difference with a faultless six penalties and one conversion after both teams scored a try each.
Neither side was able to cross the tryline in the first half, with Taylor kicking his team to a 12-9 halftime lead, while fullback Jason Woodward collected the Rebels' points.
The home side had plenty of possession but too often they released the pressure on the Crusaders with an error or poor kick while an adverse penalty count did them no favours.
The Crusaders' defence was rock solid, with Rebels prop Laurie Weeks coming off second best as he knocked himself out taking the ball up late in the first half and didn't return.
The Kiwis scored their only try in the 56th minute hooker Ben Funnell going crossing wide out.
The conversion and then another penalty from Taylor pushed Canterbury's lead out to 13 points and while there was still time to make amends, Melbourne never really looked comfortable.
The Rebels finally scored their try with two minutes remaining with flanker Scott Fuglistaller plunging over the line after the forwards had mauled the ball.
Bryce Hegarty added the extras to ensure an important bonus point for finishing within seven points.
Compounding the disappointment, the Rebels lost fullback Woodward eight minutes into the second half with a leg injury.
Crusaders coach Todd Blackadder said his team got what they needed.
While disappointed with the attack he praised his team's defence.
"Off the back of not having a potent attack tonight we defended with our hearts and it probably made the difference in the end," Blackadder said.
"We can go into the bye next weekend in pretty good nick and we need to put a lot of work into our attack and there are a few things we can do which will certainly improve our game."
Rebels coach Tony McGahan said the Crusaders' experience got the better of his team.
"They were just a bit cuter than us in certain aspects and they controlled things really well," he said.
"We kept coming back and they kept slipping away."
Final Score Rebels 19 (9) Crusaders 25 (12)
Tries - S.Fuglistaller
Pen - J.Woodward 3, B.Hegarty
Con - B.Hegarty
Tries - B. Funnell
Pen - T.Taylor 6
Con - T.Taylor
Referee: James Leckie
Assistant Ref 1:Andrew Lees
Assistant Ref 2:Ian Smith
TMO : George Ayoub
1. Toby Smith,2. Pat Leafa,3. Laurie Weeks,4. Hugh Pyle,5. Luke Jones,6. Sean McMahon,7. Scott Fuglistaller,8. Scott Higginbotham (C),9. Luke Burgess,10. Bryce Hegarty,11. Tom English,12. Mitch Inman,13. Tamati Ellison,14. Lachlan Mitchell,15. Jason Woodward
Replacemets : 16. Shota Horie,17. Max Lahiff,18. Paul Alo-Emile,19. Cadeyrn Neville,20. Colby Fainga'a,21. Ben Meehan,22. Angus Roberts,23. Telusa Veainu
1. Wyatt Crockett , 2. Ben Funnell , 3. Owen Franks , 4. Luke Romano , 5. Samuel Whitelock , 6. Luke Whitelock , 7. Matt Todd , 8. Kieran Read (c) , 9. Andy Ellis , 10. Colin Slade , 11. Johnny McNicholl , 12. Tom Taylor , 13. Ryan Crotty (vc) , 14. Nafi Tuitavake , 15. Israel Dagg
Replacments : 16. Codie Taylor , 17. Tim Perry , 18. Nepo Laulala , 19. Dominic Bird , 20. Jordan Taufua , 21. Mitchell Drummond , 22. Kieron Fonotia , 23. Nemani Nadolo