Riding the AIM Racing R6 Yamaha, the Scottish ace fought his way through the pack after being delayed on the opening lap by a crash.
And he eventually took the chequered flag by a convincing 25 seconds to claim his first-ever international race
win.
Opening qualifying on Thursday saw Amor slot into second place in the 600cc division, and 18th overall, which was just over a second behind the pace-setting German rider Rico Penkofer.
However, with cooler conditions in Friday morning's session, which got underway at 7.30 a.m., almost all of the field went considerably quicker.
Amor duly took more than two seconds off his time around the 3.8-mile Guia circuit to top the class, although Penzkofer was just 0.081s behind.
However, the much-anticipated dice between the two Yamahas on Saturday ended on the opening lap of the 15-lap race, held in sweltering conditions, when Penzkofer and Dan Linfoot, third in qualifying, crashed out at Lisboa Corner.
Amor, held up considerably in the ensuing melee, dropped close to the back of the field but soon re-grouped and gradually clawed back the advantage of new rivals Gerard Muteau and Joao Fernandes.
And, with a series of fastest laps, he soon overhauled his fellow 600cc competitors and promptly disappeared into the distance for an excellent win, which also saw him finish in 11th place overall.
"I had a feeling it was going to be a bit tricky going in to the first corner so I hung back a wee bit to stay out of trouble and, although I got held up by the crash, it paid dividends," said Amor.
"I think I was fourth from last by the time I got going again so I knew I had to get my head down. But when I started to see bikes in front of me I was able to reel them in and, once I'd got the lead of the class,
I was able to pull away.
"It was a hard race with the heat being so high but the bike was an absolute missile and the team worked so hard to give me such a great bike.
"I've got to say a big thank you to Alastair Flanagan for giving me the opportunity this week and to everyone at AIM Racing and Dunlop for all their support."