Querrey, 29, had played three successive five-set matches to reach his first Grand Slam semi-final, and nearly forced a fourth before Cilic finally saw off the American's challenge.
A journalist in a news conference said Sam Querrey was the first U.S. player to reach a Grand Slam semi-final since 2009 after beating Murray on Wednesday.
In 2016, the Swiss lost in the Wimbledon semi-finals to Milos Raonic.
Cilic won the US Open in 2014 but had never made it to a final in another Grand Slam. The court is still playing quite fast.
The third set was equally tight, a break apiece in the third and fourth games with another tiebreak required.
He pocketed the opener when Berdych miss-hit and ballooned the ball wide.
GETTYSam Querrey lost 3-1 on sets to Marin Cilic in their semi-final
After winning the first set, Federer got off to a shaky start in the second before recovering in the middle and denying Berdych a break, eventually sealing his 90th win at the All England Club. The U.S, has not had a male Grand Slam champion in the 2010s, but Querrey almost making the men's final has people hopeful that they aren't down and out yet.
This seemed a different Berdych than previously, the Czech muttering to himself and closing his eyes with intense focus between games with the clear belief that he could win.
Victory was his in the 10th game when Berdych netted a tired forehand.
Federer reached the final without dropping a set during the fortnight. I believe when coming at these stages of the tournament, I'm going to still be able to play great tennis.
"It's a really exceptional tennis player that we have, that our sport has right now", he said of Federer. Still, nothing could stop another tie-break where Federer again came out strong with an early mini-break.
"It's helped me to play better on all other surfaces". I know Marin really well.
"I'm feeling a positive on the court".
"(It) kind of deflated me a little bit.
Federer got to the ball and while looking the other way, flicked the ball across the net for an astonishing victor that forced the commentator to say, "Oh poor, Tomas".More news: LA Galaxy tight-lipped on Ibrahimovic after talk of 'huge' announcement