Loeb finished 2mins 00.1sec clear of Latvala, with Hirvonen at 2mins 31.4secs, to claim the 74th win of his career and strengthen his lead at the top of the World Rally Championship drivers' table.
Having led from the first timed practice on Thursday, Loeb proved again he is at home on the twisting roads around Trier in the Moselle valley having first won the Germany rally in 2002.
The 38-year-old Citroen driver opened a 20 second lead on Friday and extended the gap on Saturday as his Ford rival Petter Solberg damaged his car's rear-right suspension hitting a rock after an error.
Loeb went into the final day with a lead of 1min 42sec and won the ninth rally in the WRC schedule by taking nine of the 15 stages including the final one Sunday on the streets of Trier.
"The Rallye Deutschland is a race where it is easy to make mistakes," said Loeb.
"A lot of drivers have made them. This is a tricky rally with narrow roads.
"We managed to not make a mistake from the beginning and I drove very clean.
"The result is there to see."
The next event on the WRC calendar is the Wales Rally Great Britain starting on September 13 in Cardiff, the 10th of 13 in a season which culminates in Spain's Rally de Espana on November 11.
Rally of Germany final standings after Sunday's three special stages:
1. Sebastien Loeb (FRA/Citroen DS3) 3hr 41min 52.4sec, 2. Jari-Matti Latvala (FIN/Ford Fiesta RS) at 2:00.1, 3. Mikko Hirvonen (FIN/Citroen DS3) 2:31.4, 4. Mads Ostberg (NOR/Ford Fiesta RS) 3:24.4, 5. Chris Atkinson (AUS/Citroen DS3) 9:10.4, 6. Sebastien Ogier (FRA/Skoda Fabia) 9:50.8, 7. Andreas Mikkelsen (NOR/Skoda Fabia) 12:22.7, 8. Nasser Al Attiyah (QAT/Citroen DS3) 12:50.4, 9. Daniel Sordo (ESP/Mini) 14:17.3, 10. Mathieu Arzeno (FRA/Peugeot) 15:19.7
Selected:
11. Petter Solberg(NOR/Ford Fiesta RS) 21:06.4
Stage winners:
Loeb (SS1, SS2, SS3, SS5, SS7, SS9, SS12, SS13, SS15), Latvala (SS4, SS6), Sordo (SS8), Tanak (SS10, SS11), Solberg (SS14)
Drivers' standings:
1. Sebastien Loeb (FRA) 199pts, 2. Mikko Hirvonen (FIN) 145, 3. Petter Solberg (NOR) 104, 4. Mads Ostberg (NOR) 102, 5. Jari-Matti Latvala (FIN) 87, 6. Evgeny Novikov (RUS) 55, 7. Martin Prokop (CZE) 38, 8. Thierry Neuville (BEL) 32, 9. Sebastien Ogier (FRA) 31, 10. Dani Sordo (ESP) 31, 11. Nasser Al-Attiyah (QAT) 27, 12. Ott Tanak (EST) 26, 13. Armindo Araujo (POR) 11, 14. Chris Atkinson (GBR) 10, 15. Francois Delecour (FRA) 8
Constructors' standings:
1. Citroen Racing 320pts, 2. Ford Motorsport 195, 3. M-Sport (Ford) 123, 4. Qatar WRT (Citroen) 59, 5. Citroen Junior Team 52