Armitstead's 10km solo effort saw her cross the line 29 seconds ahead of team-mate Chantal Blaak who won the rest of the bunch sprint from Cromwell.
The current world champion said a lonely finish was not the plan for today.
“That wasn't the plan at all. When I was away I was almost hoping they would catch me. I was out there way too long.”
She applied the pressure on the fifth and final cobbled sector the Lange Munte.
“It wasn't an attack, It was people messing around and watching each other and not watching me, which never happens, so that was really cool. I went to the front of the group and accelerated and somehow ended up on my own," she said.
Gracie Elvin (ORICA-AIS) initially joined Armitstead, widening their gap to 45 seconds but Armitstead said Elvin wasn’t sharing the work.
“It was really frustrating to me. I thought, well, we still have the numbers to play behind, I'm not working if you’re not working. We stopped completely in the road and looked really stupid. But there was a slight drag in the road. I attacked Gracie, and I never looked back.”
Cromwell was disappointed that the move of Armitstead's stuck.
"It was quite interesting how her move went away because we were a group of 10 and she rolled off the front it was not as if she attacked. And then you've just got a small gap and she's going to take that if she can. When you have that jersey it gives you extra power," she said.
Blaak said the chase group hesitated.
“Wiggle and Rabo started riding. They kept Lizzie at a certain distance but they couldn't close it completely. We were waiting because we know when it comes back, we might need to attack again.”
In an early ten-rider breakaway, Boels-Dolmans had three riders with Armitstead, Blaak and Megan Guarnier. Over the Molenberg, Ellen van Dijk rolled away, Romy Kasper led a fragmented bunch just beyond the Paddestraat. But ultimately a 23 rider group rode together before Armitstead's attack.
Happy with third, 2013 Omloop winner Cromwell could not hide her disappointment with not taking the win.
"Omloop's my favourite race. But I'm looking ahead to Strade Bianche next week and the Tour of Flanders," she said.
Despite a 1-2 effort and Evelyn Stevens's successful hour record in Colorado, Boels-Dolmans like BMC in the men's race, didn't have everything their own way. Van Dijk crashed earlier in the race.
Armistead was confident in her and the team's form today.
“I’m really happy It’s always nice to start a season with a win. It makes the rest of the wins easier," she said.