"This doesn't change much, but it feels great to win the title," said the matter-of-fact world number one after claiming his first trophy of 2008.
"Under the circumstances, I wish he could have finished it up. This is the first time in 70 or 80 (71 actually) finals that I've played and someone gave up.
"You don't hope for it, it's unfortunate."
Federer improved his record against the world number four Russian to a prefect 12-0 as he won only their third encounter on clay.
The Swiss, who will hope to continue his progress with new coach Jose Higueras in the Monte Carlo Masters next week, called his 54th career title "a great start to the clay season.
"I haven't won one on clay in awhile (Hamburg, May 2007). And to win here on my first appearance is just great."
The success bodes well for Federer's work this week with Higueras, brought on board on a trial basis. Federer will work with the past master from Monday when he play Monte Carlo.
"It's a good week to start with, he's happy for me," Federer said of his mentor. "You go match by match and hope to play well.
"There was not a lot we could work on. Now we're off to Monaco and we hope for another good week over there."
Davydenko took a medical timeout after losing the hour-long first set as Federer saved a pair of set points and then held on as the Russian whittled away a 5-1 lead in the tiebreaker.
Davydenko packed it in as he led 2-1 in the second on serve.
"Nikolay said he felt something in back of his leg. I saw him holding it at change of ends," said Federer. "It's unfortunate. I congratulated him on a great run he had (11 straight wins including Miami).
"It a pity for both of us to finish this way.
"I wish I could celebrate with a nice match point. You walk to the change of ends and he shakes your hand - it's not the peak of emotions.
"I'm still proud and happy I could win this event."
Federer looks to have gotten his season at least partly on track after suffering with illness during the Australian Open and producing only two semi-finals so far this season.
Federer lifted his last title in Shanghai five months ago at the Masters Cup.
In the women's event, Russian Maria Kirilenko claimed the singles a day after winning the doubles as she beat Czech Iveta Benesova 6-4, 6-2.
"I feel great, this has to help my confidence," said the 20-year- old. "I've only started my clay season, this will help me on the way to Roland Garros. I've had wins in nine matches this week."
By Bill Scott, dpa