Abu Dhabi Total team's Meeke, hailing from Northern Ireland, finished a comfortable 29.1 seconds ahead of Volkswagen's Latvala to be only the sixth non-Nordic driver to claim the win here.
It was a memorable day for the Abu Dhabi Total team as they enjoyed not only Meeke's win but also the first ever podium place for Craige Breen, who finished third, 1:12.2m behind Latvala.
The 26-year-old Breen, who is a former WRC junior champion, was competing only in his fourth WRC rally.
"What a result. What can I say... It's been an exceptional weekend - something just clicked from the first stage," an emotional Meeke, who struggled to hold back his tears, said after his win.
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"It's a bit crazy to be honest. This is the home of rallying and Ouninpohja is the holy grail of rally stages. To win it as we did - incredible. I've been dreaming of this since I was a kid and I felt like that again, just playing and having fun.
Latvala said he was disappointed with the result.
"I thought I could win this event but I couldn't do it. I couldn't get the best feeling today and I could not get the Power Stage. My driving just wasn't on the same level as last year, but at least we got good points," he said.
"I can't believe it! It's been such a road to get here. I'm missing the main man [Gareth Roberts] and I know he's looking down on this now. Thank you so much everybody. I'm so proud of what we've achieved."
Volkawagen's triple defending champion Sebastien Ogier, who missed a podium for the second consecutive time this season owing to crash on the opening day, was still leading the drivers championship with 143 points.
The Frenchman was followed by Volkwagen's second team's Andreas Mikklesen (98), who finished seventh behind Hyundai's Thierry Neuville (4th) and Hayden Paddon (5th) and Ford's Mads Ostberg. Esapekka Lappi was eighth followed by Kevin Abbring and Teemu Suinen.
Volkswagen were still leading the manufacturers' standings with 196 points, followed by Hyundai (135), M-Sport World rally team (100), Volkswagen II (99) and Hyunday Motorsport N (78).