Meeke took his second WRC win by a margin of 29.7 seconds and led the way from Friday morning's second stage to the finish.
His victory was the first for a Briton in Portugal since Richard Burns achieved the same feat in 2000.
The Northern Irishman took advantage of the running order on Friday, and the benefit of others road sweeping for him, before driving more conservatively on Sunday's stages to secure his result ahead of Andreas Mikkelsen.
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Mikkelsen overcame current world champion Sebastien Ogier, who has now gone three rallies without a win, for second despite the Frenchman having been Meeke's main rival for most of the weekend.
Ogier was never able to mount a serious challenge for victory, and was eventually drawn into a battle for second with Volkswagen team-mate Mikkelsen and Hyundai's Dani Sordo.
Mikkelsen proved the faster driver on Saturday's afternoon loop to close on the Frenchman, before finally overhauling him for second on Sunday's Vieira do Minho stage when the champion had a puncture. A powerstage win for Ogier made no difference.
Sordo was unable to show the same level of pace, and fell away from the battle to take fourth behind Ogier at rally's end.
Eric Camilli was an impressive fifth, with Rally Portugal's attrition aiding his charge as well as strong pace.
That attrition hampered Camilli's M-Sport team-mate Mads Ostberg, who fell away from the top five after damaging his car and running in front wheel drive for most of Saturday.
Those woes allowed a recovering Jari-Matti Latvala into sixth overall ahead of Ostberg, but the Finn had to bounce back from broken power steering earlier in the rally.
The most dramatic trouble befell Rally Argentina winner Hayden Paddon.
He rolled on SS5, with his i20 WRC catching fire spectacularly and burning out within five minutes.
Both Paddon and co-driver Jonathan Kennard escaped without injury.
Team-mate Thierry Neuville got on the pace after a sluggish start, only to run out of fuel on Saturday's morning loop.
Meeke's team-mate Stephane Lefebvre was on course for the top six before retiring when he hit a rock.
Martin Prokop finished eighth, ahead of WRC2 winner Pontus Tidemand.
Tidemand won by an impressive margin of 1m28.8s, recovering from a puncture on Saturday afternoon that briefly allowed Nicholas Fuchs the class lead.
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