Cort finished ahead of Rudiger Selig (Bora Hansgrohe) and Jens Debusschere (Lotto-Soudal) at the end of the 190.9km one-day race held in and around Almeria, Spain.
This is the second victory this season for the 24-year-old, who earlier won a stage in February's Tour of the Valencia.
“It is a really great feeling to win again,” Cort said. “It was a long race and the team were fantastic in the finale, I couldn’t have asked for a better lead out and I am really happy that I could finish it off.”
Wim Van Rooy (Vlaanderen), Berden De Vries (Roompot) and Timothy Dupont (Veranda Williams) established the break of the day as the peloton was content in allowing only so much space before ending their run with 40km to go.
Orica-Scott stayed in the mix at the front of the race as it reached its conclusion before Cort was led out in turn by team-mates Jens Keukeleire, Mat Hayman and Luka Mezgec.
“Once the breakaway came back we stuck to our plan religiously," Orica-Scott sporting director Laurenzo Lapage said. "Magnus is full of confidence after a great start to the season with his win last week in Valencia and you could see that with the way he finished it off today.
“At the halfway point we decided how we would like to approach the finish and it’s very satisfying to see the guys not only execute the race plan but execute it perfectly and come away with the win. It bodes well for the rest of the season, that’s for sure.”