On the eve of the announcement of the preliminary squad for three Tests against the British and Irish Lions, likely selections Polota-Nau, flanker George Smith (knee) as well as centres Christian Lealiifano (leg), Rob Horne (eye) and Pat McCabe (leg) left the field injured.
There was better news for the watching Wallabies coach Robbie Deans in the performance of Waratahs playmaker Berrick Barnes, who came off the bench at half-time to score a fine individual try, set up another and kick seven points.
The victory, sealed by winger Peter Betham's try six minutes from time, kept the Waratahs in the hunt for a spot in the Super Rugby playoffs and delighted skipper Dave Dennis.
"We were probably off in a few areas but still won the match, that's something we've been working on," the flanker said in a pitchside interview.
"It was always going to be physical so you were always going to get those sort of injuries."
Smith, who had been expected to be recalled for the Lions series, led the Brumbies back row who dominated the breakdown before his departure, which had prevented the Waratahs from getting the quick ball their new attacking style required.
The Brumbies started the brighter and number eight Ben Mowen did his Wallabies chances no harm by crashing over the line to score the first try of the match after 22 minutes.
Centre Tevita Kuridrani then charged down Waratahs winger Drew Mitchell's defensive kick three minutes before half-time to send the visitors into the break 13-6 up.
Barnes, who had played less than a half of rugby this season because of injuries, came on as a half-time replacement for Horne, though, and had an immediate impact.
Five minutes after the break, he drew two defenders and drilled a brilliant pass to flanker Michael Hooper, who turned on the afterburners to score in the corner.
Barnes converted to square up the scores at 13-13 and then put the home side ahead with a penalty before Brumbies full-back Jesse Mogg converted three penalties in 10 minutes to give his side a 22-16 lead with 17 minutes to play.
Two minutes later, though, Barnes glided through the Brumbies defence and crashed over the line under two tacklers to put the Waratahs within a point of the lead.