Cilic is aiming to be come the first man since Pete Sampras in 1995 to win both the singles and doubles titles.
Cilic, the 2012 champion, had earlier defeated Luxembourg's Gilles Muller 6-3 5-7 6-4.
The Croatian is the only player remaining from the top five seeded players in the preparatory event for Wimbledon, which starts on July 3. Cilic then secured a vital break at 3-3 in the third set.
For Lopez, it would be fair to say the trophy was extra special.
In the deciding tiebreaker, Lopez saved a match point when trailing 6-5 with a stretching forehand volley, before sealing victory at the third opportunity.
"I am probably playing my best tennis", Lopez said.
"It is true that I'm going into Wimbledon with a lot of confidence".
Despite playing that one bad service game, the former world number 17 was comfortable on his serve, and he served to stay involved the opening set with a hold to love.
Cilic will face either Grigor Dimitrov or Feliciano Lopez in the final.
"It's a gift to be in this final again", Lopez, who looked close to tears at the end, told reporters.
Querrey, ranked 28th, has impressive pedigree on grass after lifting the Queen's trophy in 2010 and memorably shocking Novak Djokovic at Wimbledon a year ago.
After exchanging tiebreak wins, Lopez and Berdych played out a high-quality decider.
"We had a great battle in the 2014 final so I knew it would be tough", said Lopez, referring to a match that featured three tiebreakers.
"I'm being a little bit more motivated, and that is driving me a little bit more to be aggressive on the court, which is extremely important in my own sense", Cilic said. The Spaniard was down match point and he'd need to make a flawless shot to stay alive. He was in the same position at The Queen's Club that year in the final against Dimitrov and lost the point and eventually lost the match.