Down a set and a service break in the second, the Swiss top seed turned the match in the blink of an eye, winning 13 consecutive games to take the next two sets, then keeping the Russian at bay in the fourth as shadows crept across Rod Laver Arena.
By ending Davydenko's 12-match winning streak, which included victories over Federer in their previous two meetings, the Swiss reached his 23rd successive grand slam semi-final since he was knocked out of the third round of the French Open in 2004.
"I played him many times and I know that he goes through phases at times, very rock solid phases," Federer said. "I knew he wasn't going to play through three or four sets like that. I knew he was going to dip a little bit."
Davydenko, who thumped his first three opponents before grinding a five-set victory over Fernando Verdasco, was immaculate early, breaking Federer three times to wrap up the first set and race to a 3-1 lead in the second.
When given four chances to take a two-break lead, though, the Russian blew them all, following a double-fault with three consecutive unforced errors. Federer, sensing the momentum shift, pounced. At the end of a breathtaking half-hour of near faultless shot-making, the Swiss master emerged with a set up with a 2-0 lead in the fourth, while Davydenko was left reeling.
Davydenko then rallied, firing three crisply-hit winners in a row to save match point and break back to 5-5.
The 15-time grand slam champion bided his time, however, to take the break back, then dispatched the Russian with a thumping serve after setting up match point with an ace.
Federer now faces Frenchman Jo-Wilfried Tsonga who beat Serb Novak Djokovic in five sets 7-6 (10/8), 6-7 (5/7), 1-6, 6-3, 6-1.