A tyre malfunction saw the 24-year-old rider fly off his bike early on the first lap but his time of 1:02.30 hours was enough for victory, with Matt Bottrill and Ben Swift second and third respectively.
"It was my first crash in a time trial, I was racing without any information on power or speed and only had my gears as reference," Dowsett said.
"But I knew that as long as I could get settled I could still do a good job. Once I knew I was five seconds up half way round I knew I could do it.
"I was up quick after the crash. My hands were suffering the most, I couldn't grip the bars. I just had to grin and bear it.
"When I first took this jersey, I think it was Wiggins who said 'whoever takes this is only looking after this for me.' But I'm going to have this for three years now and I'm becoming quite attached to it."
Sam Harrison successfully defended his Under-23 title as he finished in 44:47.965 minutes.
National Time Trial Results:
1 Alex Dowsett (Movistar Team) 1:02:30
2 Matthew Bottrill (www.drag2zero.com) 0:00:20
3 Ben Swift (Sky Procycling)
4 Douglas Dewey (Hennebont Cyclisme) 0:00:33
5 Luke Rowe (Sky Procycling) 0:00:49
1 Joanna Rowsell (Wiggle Honda) 0:49:26
2 Lizzy Armitstead (Dolmans Boels) 0:00:32
3 Katie Colclough (Specialized-lululemon) 0:01:37
4 Emma Trott (Dolmans Boels) 0:01:56
5 Laura Trott (Wiggle Honda) 0:02:01
1 Sylvain Chavanel (Omega Pharma - Quickstep) 0:56:48
2 Jérémy Roy (FDJ) 0:02:01
3 Johan Le Bon (FDJ) 0:02:20
4 Jérôme Coppel (Cofidis, Solutions Credits) 0:02:31
5 Sandy Casar (FDJ) 0:02:34
1 Brian Vandborg (Cannondale Pro Cycling Team) 0:48:44
2 Rasmus Christian Quaade (Team Tre-For) 0:00:06
3 Rasmus Sterobo (Team CULT Energy) 0:00:49
4 Alex Rasmussen (Team Garrmin-Sharp) 0:00:51
5 Lasse Norman Hansen (Blue Water Cycling) 0:00:55
1 Edvald Boasson Hagen (Sky Procycling) 0:36:04
2 Thor Hushovd (BMC Racing Team) 0:00:27
3 Reidar Bohlin Borgersen (Joker Merida) 0:00:42
4 Truls Engen Korsæth (Lillehammer CK) 0:01:03
5 Kjetil Johansen Amundrud (Asker CK) 0:01:18
1 Lieuwe Westra (Vacansoleil-DCM) 1:03:59.10
2 Niki Terpstra (Omega Pharma-Quickstep) 0:00:04.51
3 Tom Dumoulin (Argos-Shimano) 0:00:40.86
4 Lars Boom (Blanco Pro Cycling) 0:01:03.08
5 Stef Clement (Blanco Pro Cycling) 0:01:20.08
1 Fabian Cancellara (RadioShack Leopard) 0:50:35.391
2 Martin Elmiger (IAM Cycling) 0:00:59.228
3 Reto Hollenstein (IAM Cycling) 0:01:57.177
4 Marcel Wyss (IAM Cycling) 0:02:28.282
5 Claudio Imhof (Atlas Personal-Jakroo) 0:05:47.319