Second seed Federer, a title winner in Melbourne on four previous occasions, never looked trouble by the Russian en route to a routine 6-3 6-4 6-4 win.
On paper, Davydenko had the potential to cause Federer a few problems. However not since 2010 - the same year he beat the Swiss back-to-back - has Davydenko been in the top five of the world rankings.
And it showed as Davydenko, now down at 40 in the current standings, was outclassed for long periods of the second-round clash.
Sixth-seeded Juan Martin Del Potro also registered a convincing three-set victory - with Benjamin Becker blown 6-2 6-4 6-2.
The 31-year-old German has never made it passed the second round in Melbourne and he never looked like altering that as del Potro dominated from start to finish.
Richard Gasquet completed a good evening session for the seeds as he overcame Alejandro Falla.
The ninth seed from France eased to a 6-3 6-2 6-2 against the 29-year-old Colombian.