Sharing Prema's Oreca 07-Gibson with Juan Manuel Correa, Deletraz and Habsburg took the chequered flag by a dominant margin of 49 seconds in mixed conditions to give the Italian outfit its fourth win in six races this season in its first season of LMP2 competition.
It marks a second successive ELMS title for Deletraz, who was part of last year's title-winning effort with WRT.
Correa only rejoined the team for the final two races of the season after suffering an injury in his parallel FIA Formula 3 programme, with the Portimao event marking his first victory.
Lorenzo Colombo, who drives for Prema in the FIA World Endurance Championship, replaced Correa for the opening four races and helped the team to victories at Paul Ricard, Imola and Barcelona.
Prema went into the Portimao race with a 24-point lead and only needing a single point to put the championship out of reach of its rivals, having narrowly missed out on wrapping things up with a round to spare at Spa.
After a cautious opening stint from Correa, Habsburg powered into the lead once he had taken over at the wheel, leaving Deletraz to close out the victory amid the pressure of knowing that the only car that could deny Prema the title, that of Panis Racing, was running in second.
"It was hard because they gave me the car with a big lead and said, now I just have to drive it to the end, the Panis team is second, and they'll never catch me, but if I put it into the wall, or we have an issue, we lose the championship," recalled Deletraz.
"It was the longest hour and 10 minutes of my life. I really wanted this title, and I took zero risks, just driving, driving, driving. It was very intense because I didn't have to push, but when you don't push, it's where mistakes happen."
Habsburg added: "We had everything to lose, the track always had a little spray and water, and a few cars spinning. It's the worst when you just want to have a simple race, but in the end, I felt so confident in the car, and it's easy to do such a good job with such a good car."
Second place allowed Panis trio Job van Uitert, Julien Canal and Nico Jamin to secure the runner-up spot in the standings and join Prema in securing an automatic invitation for next year's Le Mans 24 Hours.
Cool Racing trio Nicolas Lapierre, Niklas Kruetten and Ye Yifei completed the podium in third place, with the Swiss squad getting an auto-invite for Le Mans courtesy of its title win in the LMP3 class.
Porsche squad Proton Competition and Ferrari teams Kessel Racing and Iron Lynx took the three auto-invites on offer in the GTE class.
Iron Lynx trio Sarah Bovy, Michelle Gatting and Doriane Pin made a piece of history by becoming the first all-female crew to take an ELMS class win.
