All Blacks centre Rieko Ioane suffered a head knock in a collision. Coach Vern Cotter said Ioane was fine after the game. His head cleared quickly after he stood up, but he would go through the usual HIA process.
Captain and flanker Dalton Papali'i left the field with an ankle injury.
He took a cautious view of it and would ice it up to help it recover.
Papali'i was keen to be available to play the Crusaders, and while the defending champions were suffering, he had been on the receiving end so often that he was well aware of their threat.
But before then, it will be a case of reviewing their effort in Sydney.
Cotter said, "It was a tough game. They didn't give up, they were in there the whole time. We dominated and had two tries disallowed and didn't execute at 100 per cent. We didn't get the score margins to break the game up. It was always tight, they were a good team the Waratahs."
Cotter was disappointed the Blues didn't get rewarded for their domination towards the end of the first half and in the third quarter. Against that, the Waratahs also defended well.
"We left 15 points out there from kicks. We weren't getting the break we needed. We weren't accurate enough in our kicks and sometimes in our execution."
The loss of Ioane and Papali'i was another factor that made it a difficult night.
But Cotter said he enjoyed a night like that because the Blues had to guts it out and rely on each other to get the team through.
They had adapted after giving away three consecutive penalties.
"We were making it hard for ourselves, giving away field position and offering them the ball. In the second half, we were much more disciplined. There was an adjustment made by the team which was important. It kept us in the game. When you defend well, and the guys can rely on each other, and you don't do anything silly around that ruck area or get offside, you can generally get the ball back.
"We'll take the win but acknowledge that it was a good team opposite us."
First five-eighths Stephen Perofeta had a poor night with his kicking boot, but Cotter said he was confident work he was doing on his kicking would prove fruitful, and he was pleased Perofeta wanted to keep on kicking to find a way through.
Papali'i said it was clear the Waratahs had stepped their game up compared to last year.
"The game could have gone any way and we just scraped in there. They're a physical team and they're performing."