Fullback Perofeta was feeling his shoulder while Laulala incurred a calf problem during the 55-21 win at Eden Park on Saturday.
Coach Leon Macdonald is hoping the damage isn't too serious.
"Both look relatively significant," he told journalists.
"Stevey felt his shoulder move a little bit so we need to get a scan on that. I think he's done something to that shoulder in the past so he'll be sweating on that.
"And Nepo's calf doesn't look 100 percent great as well."
The injury to Laulala continues to a run of injuries to All Blacks prop candidates, with Crusaders pair George Bower and Fletcher Newell having both been ruled out for the rest of the Super Rugby season.
The injuries were among the few black marks for a Blues side who overwhelmed the Waratahs with their physicality in a seven-try display.
The scores were level after half an hour but the passes began to stick after that for a Blues side prepared to run the ball from deep.
Winger Caleb Clarke was their most dangerous attacker and scored a try, while Zarn Sullivan - who replaced Perofeta - made numerous strong surges and bagged a brace.
Hooker Ricky Riccitelli also crossed twice, continuing his prolific try-scoring form this season, primarily from close range.
The result cements the Blues' fifth position ahead of next week's trip to Lautoka to face the Fijian Drua, while the Waratahs have slumped to 10th.
Blues player Caleb Clarke celebrates his try with Beauden Barrett during the Blues v Waratahs Super Rugby match at Eden Park. Photo: Photosport