The South Australian attacked over a climb on the final lap of the gruelling 179km stage from Mohelnice to Šternberk, winning the stage in a duel with Markus Hoelgaard (Unox-X), the only rider who could stick with Howson.
Howson's attack capitalised on the earlier hard work of Jack Bauer and Michael Hepburn to bring the gap to the race leaders down to below one minute by the final circuit as the day's break contained threats to the general classification.
With Sunweb then animating the race, it was all back together by the time Howson unleashed.
“I just had to match anyone on the climb on the last lap," the 27-year-old said. "When the Uno-X guy rode a super hard tempo there was only us two left and then it was a matter of playing my move right into the final to get my hands in the air.
“It’s awesome, it’s been a long time coming, I guess. I put some hard work in in the last couple of months and it’s nice to see that pay off.
The Aussie registered squad dominated the race in the Czech Republic with a Mitchelton-Scott rider in the leaders' jersey on every stage after rocketing home 35 seconds ahead of Team Sunweb in the 18.6km team time trial on the opening day.
Luke Durbridge handed it over to team mate Kaden Groves after his top 20 finish on Stage 3 propelled him into the lead.
But it was always the plan to secure victory for Howson.
"I can’t reiterate enough," Howson said. "The guys here, kicking it off with the team time trial and the way they’ve ridden the last couple of days, it’s truly amazing to sit behind these guys and see what they’re able to do. It was my way of repaying them with the stage win and the GC.”
Mitchelton-Scott sport director Dave McPartland was impressed with his team's performance.
"This was the goal at the start of the week, we had lofty goals with the GC and stages, and we ticked both boxes there. We had it taken to us a bit more than last year, there was a lot deeper field than last year, but we came away with two wins and the overall.”
Watch Howson in action at the Criterium du Dauphine Wednesday 12 August - Sunday on SBS Viceland and streaming via SBS On Demand.
Mitchelton-Scott to the Criterium du Dauphine: Nick Schultz, Adam Yates, Brent Bookwalter, Jack Haig, Damien Howson, Daryl Impey, Christoper Juul-Jensen Subs: Esteban Chaves, Mikel Nieve.
The Criterium du Dauphine LIVE and FREE on SBS VICELAND and streaming via SBS On Demand:
Wednesday August 12
LIVE: Cycling: Criterium du Dauphine STAGE 1
Thursday August 13
LIVE: Cycling: Criterium du Dauphine STAGE 2
Friday August 14
LIVE: Cycling: Criterium du Dauphine STAGE 3
Saturday August 15
LIVE: Cycling: Criterium du Dauphine STAGE 4
Sunday August 16
LIVE: Cycling: Criterium du Dauphine STAGE 5
For the live TV coverage on SBS VICELAND - all stages will be live to Eastern (NSW / VIC / TAS / QLD) and Central (SA, NT) with the Central coverage crashing half an hour in.
WA will be delayed on SBS VICELAND but viewers can watch LIVE via streaming at SBS On Demand.