Greipel defeated Gerald Ciolek (MTN-Qhubeka p/b Samsung) and John Degenkolb (Argos-Shimano) in torrential rain to final win a race that has long denied him.
"I have tried so often but never won it. Going to the Tour de France with the national champion's jersey makes me very happy,” said Greipel.
In Spain, Movistar youngster Jesús Herrada was the surprise winner as he edged out Jon Izagirre (Euskaltel) for the title.
The two men were the sole survivors of a breakaway at the end of the race that had previously contained Angel Madrazo (Movistar), David Arroyo (Caja Rural), Tino Zaballa (Christina Watches) and Mikel Iturria (Euskaltel-Euskadi).
"If you told me yesterday I would be winning today, I wouldn't believe you, but I can't believe it now either," said Herrada. "I came here with the intention of doing a good race in the TT, but it didn't go well.
"This victory is for my family, for the team, for an old team-mate from my under-23 age, Rubén Cuesta, who is going through a hard time in his life, and for Rufino Murgia, who passed away today.
"This gives me confidence for the future, because 2012 wasn't a good season for me - despite the win in Asturias."
In France, Arthur Vichot (FDJ) took victory with a late attack at the end of the race.
Vichot burst clear of Sylvain Chavanel (Omega Pharma-Quick Step) and Tony Gallopin (Radioshack-Leopard) in the final kilometre to secure the blue, white and red jersey for the next 12 months.
In Belgium, RadioShack's Stijn Devolder claimed the third Belgian title of his career at the ripe old age of 33.
Devolder had time to celebrate before the finish with Gianni Meersman (Omega Pharma-Quickstep) and his team-mate Jan Bakelants coming in next.
In Holland, Johnny Hoogerland (Vacansoleil) will wear the Dutch national jersey for the first time after beating out Tom Dumoulin (Argos-Shimano) and Sebastian Langeveld (Orica-Green Edge.)
In Denmark, Michael Mørkøv (Saxo-Tinkoff ) made up for his Tour de France snub by claiming his first national victory
In Switzerland, Michael Schär (BMC) won a battle with Martin Elmiger (IAM Cycling) to win the Swiss title for the first time.
In Italy, Sunday saw the time trial take place, and there was no surprise as Marco Pinotti (BMC) won the race for the sixth time in his career.
In Britain, Mark Cavendish (Omega Pharma-Quick Step) became British road racing champion for the first time with victory in Glasgow.
Czech Republic: Jan Barta (NetApp-Endura)
Estonia: Rein Taaramäe (Cofidis)
Greece: Ioannis Tamouridis (Euskaltel)
Kazakhstan: Alexsandr Dyachenko (Astana)
Ireland: Matthew Brammeier (Champion System)
Japan: Yukiya Arashiro (Europcar)
Lithuania: Tomas Vaitkus (Orica-GreenEdge)
Luxembourg: Bob Jungels (RadioShack-Leopard)
Norway: Thor Hushovd (BMC Racing)
Poland: Michal Kwiatkowski (Omega Pharma-Quick Step)
Russia: Vladimir Isaichev (Katusha)
Slovakia: Peter Sagan (Cannondale)