Finland international Teemu Pukki, who scored twice for his country while on international duty, pounced on an attempted interception in the area from George Friend and poked the ball home via a slight deflection in the 58th minute.
It was a deserved win for Norwich as they had more of the ball and more clear opportunities than a disappointing Boro side, who rarely looked like scoring.
Pulis said: “Norwich were the better team but I think it was a clear penalty when Britt Assombalonga was brought down in the box early in the second half.
“It wasn’t given and they go up the other end and score a soft goal which had a lot to do with poor defending.
“We started the game okay and then dropped off after 20 minutes and we also started the second half poorly.
“It’s disappointing of course but this is the Championship and there’s always a chance you can get results like this. What we have got to do now is put it behind us and make sure we bounce back.”
There was a bizarre moment 15 minutes from time when Norwich defender Timm Klose was shown a second yellow card for bringing down Assombalonga when the striker was running in on goal, only for it to be withdrawn after the linesman had spotted an offside.
Norwich City: Krul, Aarons, Zimmermann, Klose, Lewis, Tettey, Leitner, Emi (Vrancic 77), Stiepermann (Trybull 82), Hernandez, Pukki (Rhodes 84). Unused substitutes: Godfrey, Marshall, McGovern, Cantwell.
Middlesbrough: Randolph, Ayala, Flint, Fry (Braithwaite 59), Shotton, Besic (Saville 53), Clayton (Hugill 70), Friend, Downing, Howson, Assombalonga. Unused substitutes: McQueen, Batth, Konstantopoulos, McNair.
Referee: J Linington (Isle of Wight).