Spain's Dani Sordo was second for Citroen, with Belgian Thierry Neuville third in a Ford.
Latvala's French team-mate Sebastien Ogier, out of contention from the opening stage due to a fuel feed problem, remained championship leader after six rounds and collected three bonus points by winning the final 'power stage'.
Poland's former Formula One driver Robert Kubica was fastest in the WRC2 category, finishing 11th overall.
Final results from the Acropolis Rally on Sunday, the sixth of 13 races in the World Rally Championship:
1. Jari-Matti Latvala-Miikka Anttila (FIN/VW Polo-R) 3hr 31min 1.2sec, 2. Dani Sordo-Carlos del Barrio (ESP/Citron DS3) at 1:50.0, 3. Thierry Neuville-Nicolas Gilsoul (BEL/Ford Fiesta RS) 2:14.1, 4. Andreas Mikkelsen-Mikko Markkula (NOR-FIN/VW Polo-R) 3:55.1, 5. Nasser Al-Attiyah-Giovanni Bernacchini (QAT-ITA/Ford Fiesta RS) 4:12.6, 6. Mads Ostberg-Jonas Andersson (NOR-SWE/Ford Fiesta RS) 5:48.7, 7. Mikko Hirvonen-Jarmo Lehtinen (FIN/Citron DS3) 8:00.7, 8. Martin Prokop-Michal Ernst (CZE/Ford Fiesta RS) 8:01.2, 9. Evgeny Novikov-Ilka Minor (RUS-AUT/Ford Fiesta RS) 8:11.8, 10. Sbastien Ogier-Julien Ingrassia (FRA/VW Polo-R) 10:10.3
Best times in the special stages: Novikov 4 (SS1, SS2, SS8, SS9), Latvala 4 (SS3, SS4 SS5, SS7), Sordo 1 (SS6), Ogier 2 (SS10, SS14), Mikkelsen 3 (SS11, SS12, SS13)
Standings from Power Stage (SS14):
1. Sbastien Ogier-Julien Ingrassia (FRA/VW Polo-R) 3 points, 2. Evgeny Novikov-Ilka Minor (RUS-AUT/Ford Fiesta RS) 2, 3. Andreas Mikkelsen-Mikko Markkula (NOR-FIN/VW Polo-R) 1