The Reds will finish on 58 points and fifth overall, irrespective of matches later on Saturday, and will face the seven-times champions, who finished fourth following their 25-17 win over the Wellington Hurricanes, in Christchurch next week.
While the Reds had their final position in the playoffs to consider, the match was also seen as part of a set of selection trials for new Wallabies coach, and current Queensland boss, Ewen McKenzie ahead of the Rugby Championship in August.
Reds flyhalf Quade Cooper was undoubtedly under most scrutiny after he was not wanted by former Wallabies coach Robbie Deans for the British and Irish Lions series.
Cooper was at his enigmatic best on Saturday.
His quick thinking, ability to involve himself in play and passing and kicking skills led to Ben Lucas' first half try while another was disallowed to Rod Davies after Luke Morahan had knocked on following a clever grubber kick from the flyhalf.
Cooper, however, was also intercepted four times, the first of which led to a Berrick Barnes try from 80 metres out after scrumhalf Brendan McKibbin had grabbed the no-look, inside pass from Cooper.
The 25-year-old's tactical kicking was also hit and miss and he was put under immense pressure by the Waratahs' defence.
Waratahs fullback Cam Crawford had scored an earlier try for the hosts, which McKibbin converted, while Cooper had opened the scoring with an early penalty.
McKibbin failed to extend the Waratahs' 12-8 lead at halftime when he missed an easy penalty early in the second half before Cooper dragged his side into a 14-12 lead midway through the second spell following two successful penalties.
Barnes had the opportunity to snatch victory with two late penalties but missed both, with the second fading wide of the left upright with 90 seconds remaining, and an attempted drop goal after the hooter sounded that sailed wide right. (Writing by Greg Stutchbury in Wellington; Editing by Justin Palmer)