It was announced on Friday that Jacobson would be coming home to recover in the hope that a long break would help him get back into the game in the 2020 season.
All Blacks coach Steve Hansen said it had been a tough decision and it was really disappointing that Jacobson had to go home.
"However, from his point of view I think medically and as a coach and doctor team there is only one decision we could have made," he said.
Jacobson, who was one of the surprise selections when the squad was announced, said it had been a tough pill to swallow. The decision had been made on Thursday night that it would be better for his career to step away now and have some time to recover and put it all behind him.
He said he had got through a Mitre 10 Cup game for Waikato without problems but had suffered a small knock against Tonga which, initially, he seemed to get through but then with travel and attempting to train on Tuesday, he felt he probably wasn't quite right.
His symptoms became obvious when exercising with dizziness and light-headedness.
"You don't feel quite right, you drop a few balls and your skills aren't probably quite there," he said.
While it was disappointing to go home, he said it was something that would happen to others during the tournament and he had just had to go home and deal with it.
The support from management and players had been great, he said. He had talked with hooker Dane Coles and fullback/wing Ben Smith who had endured similar issues and now it was a case of taking the time to fully recover so he could get back to playing the game without worrying.
Dr Tony Page said the background was that Jacobson had a concussion last year with a prolonged recovery and this year he had three in three months and while there was no single number that would make you withdraw a player, the priority was his long-term health and not getting caught up in the context of the World Cup.
Hansen said it was a hard conversation he and Dr Page had to have with him but on the other side he was 22-years-old and had been selected to come to a World Cup which was a ringing endorsement that he had an outstanding career ahead of him.
"The priority right now is we put him in a situation where he can recover to being the rugby player we know he can be. He's 22, he could get three more World Cups but his health is the main important ingredient at the moment.
"What was a tough decision really became an easy one," he said.
Hansen said Jacobson's loss was disappointing and a setback but those things happened.
"You are challenged by those adversities but it doesn't change anything that happens for the rest of our time here, we've got to get on with it. It's his misfortune and Shannon's great opportunity.
"We've seen it before, a guy like [prop] Joe Moody came in for the quarterfinals [in 2015] and ended up playing quarters, semis and final and played really, really well. We are blessed with depth and it's now going to be challenged a bit," he said.
Hansen said the week without a build up to a game at the weekend had been great for the coaching staff as they had been able to do some work that needed to be done with the time available.
"You're always time poor when there's Test matches to be played and I think we'll get the benefits of that. Whilst it's been busy, it's been good," he said.
Hansen said fellow loose forwards Vaea Fifita and Dalton Papalii had not been considered as they were injured and because the tournament hadn't started yet it wasn't a situation where Liam Squire could be considered.