The Colombian took the queen stage of the five-day race, bursting out of a small group at the end of the 208.5km stage from Clavier to Engis.
The 27-year-old German, who won the time trial gold medal at the world championships in Copenhagen last September, was eight seconds back in seventh to hold off GC rival Lieuwe Westra for the overall.
Leonardo Duque, Jacopo Guarnieri, Michael Schär and Juan Horrach escaped after 35 kilometres and were joined by Pim Ligthart, Laurens De Vreese, Jetse Bol, Maxim Belkov and Martin Kohler.
But they were reeled in with 60km to go and a nine-man counter-attack featuring Stijn Devolder, Carlos Barredo, Romain Zingle, Alberto Betancur, Sven Nys, Peter Serry, Dmitriy Fofonov, Maxime Vantomme and Amaël Moinard formed.
Barredo was a threat on GC so Omega Pharma-Quick Step's Martin put himself on the front of the chasing pack to pull everything back together.
Belgian champion Philippe Gilbert went early at the finish on the Rue Des Fagnes Engis before Kevin Pauwels made a dash for victory only for Liquigas-Cannondale's Betancur to follow his wheel and take a comfortable victory.