Benoit Paire made a remarkable Cup debut for France, outplaying an injured Pablo Carreno-Busta 7-5 6-1 6-0 in the opening rubber in less than two hours.
Steve Johnson had been due to face Cilic at the start of the day, but Querrey was drafted in to tackle an opponent who had won each of their previous six meetings.
The world No 6 was beaten in four sets, and a frustrating match was compounded when he was handed a code violation by umpire Carlos Ramos for smashing his racket.
Marin Cilic then put Croatia firmly in the driving seat, when he defeated Frances Tiafoe 6-1 6-3 7-6 (5), to put the hosts 2-0 ahead.
The world number six broke his racquet on the ground after a series of errors in a tight third set against Querrey. The Americans remained calm and they won the next three points to steal another set and move two sets to love up.
"I am good, under the circumstances", Ramos was quoted as saying in Portugal's Tribuna Expresso.
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Both Cilic and Coric had won their singles matches on Friday, before the United States cut Croatia's lead to 2-1 as Mike Bryan and Ryan Harrison beat Ivan Dodig and Mate Pavic in a dramatic doubles rubber on Saturday.
He was given the reprimand by Ramos but, because it was his first offence of the match, Cilic was issued with a warning and no points were deducted. "I really wasn't paying attention", Tiafoe said.
Croatia extended its flawless record over the U.S.to 5-0.
Spain was without top-ranked Rafael Nadal, who was ruled out because of the right-knee injury that forced him to retire from his U.S. Open semifinal against Juan Martin del Potro. France is in back-to-back finals for the first time since 1972.
He took a 6-1 lead in the second set tiebreak in superb fashion only to crumble under Querrey's onslaught with the American world number 61 winning seven straight points.
Both sides, along with France and Spain, are guaranteed a place in next year's revamped Davis Cup.