Former world number one Federer and Stanislas Wawrinka needed to win the doubles to keep the tie alive after Friday's two singles went to the US but after a good start the Swiss pair lost 4-6 6-3 6-3 6-3 to Mardy Fish and Mike Bryan.
It was payback time for Fish who suffered two heartbreaking defeats in marathon matches in last year's quarter-finals against Spain's Feliciano Lopez and David Ferrer.
"It feels pretty good to win," said Fish. "I certainly know what it's like to lose and it's not a great feeling.
"This guy is the greatest doubles player of all time and I'm just trying to play my part."
Holders Spain joined the Americans in the quarter-finals as they moved 3-0 ahead against Kazakhstan in Oviedo to give new captain Alex Corretja a pleasing start in the absence of Ferrer and Rafa Nadal.
Last year's runners-up Argentina and Czech Republic also moved smoothly through with a day to spare against Germany and Italy respectively.
Japan have an uphill battle in their first World Group tie for 26 years, 2-1 down at home to Croatia.
Federer has never won the Davis Cup and will have to wait at least another year to fill in one of the few blanks on his CV after a humbling couple of days in front of his home fans.
Having lost to big-serving world number 17 John Isner on Friday, Olympic doubles champions Federer and Wawrinka were well beaten by Fish and Bryan as the Americans, winners of the team competition a record 32 times, swept to victory.
"I thought we actually played pretty well," said Federer. "It was again a high standard from both sides with not much between us.
"We had our chances but maybe they were a touch better than us and that shows in the score. We played well for a long time but we had a couple of games when we struggled a bit too much."
United States next play Canada or France who are level 1-1 in their tie.
Spain captain Corretja was unable to call on any of the four players who beat Argentina in last year's final against the Kazakhs but his country's unrivalled strength in depth was again in evidence.
Marcel Granollers and Marc Lopez needed less than two hours to beat Evgeny Korolev and Yuriy Schukin 6-2 6-3 6-1 on Saturday after singles wins for Nicolas Almagro and Juan Carlos Ferrero on Friday had effectively put the tie beyond the Kazakhs.
"It was spectacular the way they worked together," Corretja said after Spain's 22nd consecutive home victory in the Davis Cup.
"Marcel is like a cat at the net and Marc has played some phenomenal strokes."
Argentine doubles pair David Nalbandian and Eduardo Schwank produced a stunning comeback from two sets down to kill off any hopes of a German fightback in Bamberg, beating Tommy Haas and Philipp Petzschner 3-6 4-6 6-4 6-3 6-4 to give the south Americans a 3-0 advantage.
The Czechs will have to wait until Sunday to discover who they face in the last eight after Sweden managed to take their tie against 2010 champions Serbia into the third day.
Johan Brunstrom and Robert Lindstedt battled for more than four hours to beat Janko Tipsarevic and Nenad Zimonjic3-6 6-3 7-6 6-7 10-8.
The Serbs, 2-1 up, should still clinch the tie on Sunday when world number nine Tipsarevic takes on 348th-ranked Michael Ryderstedt in the first reverse singles.
Japanese number one Kei Nishikori meets Dodig on Sunday hoping to redeem himself after a disappointing defeat by Karlovic on Friday.