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Referee Mark Lawrence described Bowe's action as cynical and with Dan Carter converting the penalty try, Ireland were 10-3 down at the interval.
"Obviously it would have been considerably better if we'd gone in at half-time level pegging. The penalty try was a kick in the teeth," said O'Driscoll.
"But we did play the majority of the first half in our own half and eventually the All Blacks will make you pay for that.
"I didn't see what happened with regards to the try but there were a few times when we scrambled well and managed to hold them out.
"I wouldn't say it was deflating at half-time but there would have been more of a step in us had we been level pegging.
"On another day we could have been the ones to get a breakaway score just before half-time. It's all about momentum.
"New Zealand are a smart team who have clever players in key positions like Dan Carter."
Ma'a Nonu and Brad Thorn crossed for New Zealand early in the second half to move the visitors out of sight and O'Driscoll was pleased Ireland did not raise the white flag.
"When they scored the third try there was potential for us to capitulate and allow them to cross the whitewash time and time again," he said.
"But we stood under the posts and said we wouldn't let that happen, not at Croke Park. We battled hard for the full 80 (minutes) and contained them."
Ireland coach Declan Kidney refused to pass judgment on the decision that spelt the beginning of the end for the hosts.
"I didn't see the penalty try but there were enough people looking at it," he said.
"New Zealand played very well and won the field position battles by a big way.
"Most of the game was played inside our half. You can only defend for so long and they took their opportunities. There were two or three more they might have scored."
New Zealand coach Graham Henry was satisfied South African referee Mark Lawrence had made the correct decision in awarding the penalty try.
"That's the law - the referee just applied the rule. It was good for us at the time," he said.
"Any try just before half-time has an influence on the game."
Henry added: "We're pleased with the result. The guys played well and we dominated the game most of the time.
"We played with tempo but were frustrated that we created chances that we didn't finish. A couple of tries went begging.
"Our defence was excellent, the best of the tour so far. We got a lot of turnover ball.
"Ireland played as well as they were allowed to. I imagine they went out with a more expansive gameplan.
"Brian O'Driscoll and Luke Fitzgerald played well, they cut us up in midfield a couple of times, but our cover defence was good."