Mr Houchen beat Labour's Sue Jeffrey by a little over 2,000 votes after second preference votes were counted. Liberal Democrat Chris Foote Wood was third and UKIP's John Tennant finished last.
Mr Houchen will have a budget of Â£15m a year.
In another result, Labour retained control of Durham County Council despite losing 20 seats.
The party won 94 seats in the 2013 election and that has now fallen to 74. Independent candidates have the second highest number of seats (28) followed by Liberal Democrats (14) and Conservatives (10).
Council leader Simon Henig said he was "very pleased" to have retained a majority in a "challenging" election.
As Tees Valley mayor, Mr Houchen will head the Tees Valley Combined Authority, made up of Darlington, Hartlepool, Redcar and Cleveland, Middlesbrough and Stockton councils.
After the declaration at Thornaby Pavilion, Mr Houchen said: "What we have seen in recent years is fantastic trends towards the Conservatives across the Tees Valley and today is, I believe, a tipping point.
"We have seen a political earthquake that's happening right here for the Conservatives across the North East.
"It's the first time anybody would expect a Conservative mayor for the Tees Valley and it is the start of five genuine target seats for the Conservatives in the upcoming general election, and I genuinely believe this is a starting point for turning the Tees Valley blue."
This is a sensational vote for the Conservatives.
Beating Labour in the first round, we perhaps thought Labour might claw it back with second preference votes. They were counted then but actually Conservatives pulled further ahead and Ben Houchen beat Sue Jeffrey the Labour candidate in a runoff to become the Tees Valley mayor.
He has now got to deliver on certain promises, one of which is to take control of Durham Tees Valley Airport and try to revive its fortunes.
He talked about turning the Tees Valley blue in the general election in just over a month's time and that will be the Conservative focus now.
Conservative Ben Houchen has become the inaugural Tees Valley mayor after winning a tightly-fought contest.