New Zealand 22
Referee Mark Lawrence awarded a penalty try after consulting with his video official and then sin-binned Bowe in a move that proved decisive.
Ireland, who had clawed their way back to level terms at 3-3 just beforehand after Ronan O'Gara cancelled out a Dan Carter penalty, were shell shocked as they went in for the break after surviving relentless All-Black pressure.
Not even the yellow card dismissal of prop Tony Woodcock for a punch on Rory Best early in the second half could inspire the Irish, who went to concede tries to Ma'a Nonu and Brad Thorn as the clinical All-Blacks closed the game out.
"Obviously it would have been considerably better if we'd gone in at halftime level pegging. The penalty try was a kick in the teeth," said Irish captain Brian O'Driscoll on a day when little went right for his side.
"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 halftime 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."
Lackluster throughout on a particularly bad day for O'Gara, Ireland did regain some credibility as they kept their opponents scoreless for the final quarter, and O'Driscoll took pride in that achievement.
"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 added.
"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 wouldn't be drawn on the Bowe controversy and the subsequent penalty try.
"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."
"That's the law - the referee just applied the rule. It was good for us at the time," he said. "Any try just before halftime has an influence on the game.
"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 defense 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 game plan.
"I don't think anyone could be satisfied with the performance against the All Blacks," said O'Leary after his second cap.
"We didn't play any rugby and we have to learn what went wrong in time for Argentina, which has become a massive game now.
"I'm disappointed, because I felt like we prepared well against New Zealand. I definitely expected more from us - we're capable of much better.
"That's a positive for the future. But it's no good talking about how good we are or about potential. We need to produce."
Replacements: J. Flannery for Best 58, T. Buckley for Hayes 77, S. Ferris for O'Connell 62, S. Jennings for Wallace 77, E. Reddan for O'Leary 68, P. Wallace for Fitzgerald 75, K. Earls for Dempsey 71.
Replacements: C. Flynn for Woodcock 68, J. Afoa for Kaino 45, P. Weepu for Cowan 59, S. Donald for Rokocoko 75, I. Toeava for Smith 65.