Pakistan had used the short ball well, to have New Zealand 99 for 6 by the 23rd over, but Flower said the death overs required a different approach.
"We didn't use our brains at all towards the end," he said. "Bowling yorkers is skill execution, and we didn't do that. They played well at the end. The short ball worked to a certain extent, but we overdid it, and we didn't learn and we just didn't bowl enough yorkers.
"If we're going to be honest we should have got them out for 200-odd, seeing the start we had."
Pakistan's seamers were guilty of bowling lengths that allowed New Zealand's tailenders get under the ball. Matt Henry and Mitchell McClenaghan struck six sixes and seven fours in what was a record 73-run ninth-wicket stand for New Zealand against Pakistan.
"You can get as many messages as you want out to the players, but it's got to come from within," Flower said. "It's also executing your skills. If there's a yorker to be bowled, you have to bowl it as a yorker, not a half volley."
Flower didn't confine his stern words to the bowling attack's performance. Pakistan's batsmen had made a slow start to the chase of 281, making just 33 runs from the first 10 overs, at the end of which the required rate had climbed to 6.2. Flower felt they could have been more aggressive.
"Even though we should have got them out for a lot less, I still backed the guys to get the target. We lacked a bit of intent at the start and then we had quite a few soft wickets. We didn't take advantage of a good batting track in the afternoon."
New Zealand have now won 9 out of 11 completed limited-overs matches in their home summer. Pakistan, meanwhile, have lost four consecutive matches on tour, having begun with a comfortable T20 victory in Auckland.
"It doesn't seem like we're learning from our mistakes - that's the disappointing part," Flower said. "It's one thing losing, but you're paid to do a job and if you keep making the same mistakes, there are going to be questions asked."
Flower praised New Zealand's "resilience" for defending 280 despite losing McClenaghan's overs through injury, and described Henry Nicholls' 82 as "mature".
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