England were in touching distance of a first win in New Zealand since 2003 in both Tests and they will head home with a sense of disappointment.
Damian McKenzie kicked two second-half penalties to overturn a deficit in Dunedin before Beauden Barrett came off the bench to inspire a match-winning fightback in Auckland after England had led by four points.
Marcus Smith struggled from the tee in the Dunedin defeat, missing three of his five shots at goal, but he orchestrated England well from fly-half and his cross-field kick has become a potent weapon.
Smith changed the angle of attack to pick out Henry Slade in Tokyo before finding both wingers, Immanuel Feyi-Waboso and Tommy Freeman, with the same method to give England the half-time lead at Eden Park.
The 25-year-old has cemented his place in the England number 10 jersey and he says the series ultimately came down to fine margins.
“It was probably the small moments – a touch at the breakdown, a few wrong decisions on the edges from myself – that turned the tie in the All Blacks’ favour,” Smith told Sky Sports.
“When they’re ahead, they’re obviously a very successful team and it’s hard to wrestle momentum back.”
New Zealand had far more caps than the more youthful English visitors and their experience told when it mattered most, as full-back Barrett and prop Fletcher Newell came off the bench to shore up the backfield and the set-piece at Eden Park.
England, though, have shown great resilience and look a different team to the one beaten for the first time by Fiji in their final World Cup warm-up in August.
“We’re building something and the belief we have is growing. On another day we get the result here, or the result last week,” said Smith.
Speaking to BBC Radio 5 Live, Borthwick added: “I am immensely proud of these young men. I think the team is making progress.
“We ultimately got ourselves in positions to win both these Test matches and unfortunately have not been able to convert.
“Experience in international rugby is really important. I can’t accelerate experience but what you can accelerate is learning.
“This is an exciting young group that has got huge potential and I think with their immense work ethic and appetite to improve, there is a very high ceiling for them.”
