New Zealand-born Hartley led England to back-to-back Six Nations titles after missing the 2015 Rugby World Cup when Stuart Lancaster dropped him following another suspension.
He has a lengthy disciplinary record, being banned in the past for a total of more than a year for offences including eye-gouging, biting and verbally abusing referees.
But Eddie Jones put his faith in him to captain England last year and Hartley played a big part in the team's resurgence after a humiliating World Cup exit.
"He's a top quality player. We had to find what we believe are the right players to select," said Borthwick, who had a close view of him through his role as England assistant coach.
"Throughout the whole squad there are going to be top quality players who missed out on selection because talent is that great now. So we are trying to get the right blend of players for what we need.
"We believe we've got three hookers there that are the right ones that we need to play the rugby we want to in New Zealand," he added.
Hartley's understudy Jamie George, who spent most of the Six Nations coming on for Hartley around the hour mark, got the nod alongside Ireland captain Rory Best and Ken Owens of Wales.
- NZN