The former Scotland defender was unveiled by United after leaving Thistle in second place in the Irn-Bru First Division, five points off leaders Morton but with two games in hand.
McNamara emerged as the leading candidate over the previous 48 hours after United spoke to the likes of Steven Pressley and Billy Dodds over the managerial vacancy created by the expedited departure of Peter Houston on Monday morning.
Thistle have been leading the First Division for much of the season and are in the Ramsdens Cup final but McNamara knew he could not pass up the opportunity.
"It has been difficult," he said. "Obviously it was a big decision to make, to leave Thistle at this time. But it's one that feels right. It says what I think of Dundee United to do that.
"It wasn't an easy decision but the things that are in place here are the things that really attracted me to the job. It's an established SPL club with a fantastic playing squad, infrastructure and youth set-up."
McNamara, who has signed a three-year contract, has only been in management since April 2011, when he initially took over from Ian McCall on a caretaker basis before securing a permanent deal a month later.
Thistle finished sixth last season and McNamara impressed by turning the Jags into title contenders on a reduced budget to earn him a chance in the SPL.
"It has come a lot quicker than I expected in my managerial career," said McNamara, who has taken assistant Simon Donnelly with him from Firhill. "You obviously want to do well and get better at things as I did as a player and go up and up.
"It has come really early on and that's why it's the right time to take it. Great jobs like United don't come around very often. It's a club with a fantastic tradition, with a lot of trophies and great players and great managers over the years."
- Sports & Recreation