However, it was a tough fight on Thursday, with the 36-year-old missing two match points in the final-set tiebreak and then saving two for Paire.
Failure by Federer to win the grasscourt title would send rival Rafael Nadal back to the top spot going into Wimbledon which starts on July 2.
The qualifier, world No 109, broke his Japanese opponent twice in the first set to take the initiative in the contest before he recovered from a 5-2 second set deficit and saved a set point to close out the match in one hour and 23 minutes.
Roger Federer conceded there was an element of fortune to his Gerry Weber Open win over Benoit Paire, even if he felt he played well in Halle.
Cilic will face Nick Kyrgios, who eliminated defending champion Feliciano Lopez 7-6 (5), 7-6 (3).
Cilic improved to 6-0 against Querrey, including three wins at Wimbledon, one of them past year in the semifinals.
Federer, who won his 18th grass-court title in Stuttgart on Sunday, is just three match wins away from matching Jimmy Connors' all-time record of 174 victories on grass.
"It's good to know that I always play well when it's needed", Federer said.
"I've never played back to back finals on grass like this in pre-leading up events before Wimbledon", Federer added.
After a firm beginning, defending champion stumbled a little in the first set which went on till tie-breaker.
Federer is bidding for a record-extending 10th trophy in Halle.
"I think in that match I played nearly ideal", Coric said looking back to Indian Wells.