The pair exchanged early breaks in overcast conditions before top-seeded Federer stamped his authority by winning the tiebreak 7-1, ending Kudla's 10-set winning streak this week.
Federer showed signs of frustration during the opening stages of second set and received a code violation for ball abuse after missing a volley at the end of a lengthy exchange.
After Dubai 2011, those are the only ATP 500 finals that Roger had lost and he will be the favorite against Borna to improve his score in the finals of this level to 21-6 and move away from Rafael Nadal who stands on 20 titles from 26 finals.
World No. 1 Roger Federer on Thursday kept his quest for a 10th Gerry Weber Open grass-court title alive by saving two match points to defeat France's Benoit Paire 6-3, 3-6, 7-6 (9/7) and make the quarter-finals. "I think Ebden played a good match and I'm happy I got through somehow". His famous one-handed backhand was on fire, striking down winners and passing shots from all corners of the court.
In the second set, Ebden broke Federer twice and served for the set at 5-4 only for the Swiss to break back for a second time. In front of a packed crowd under the roof in Germany, Federer finished with a flourish to break Ebden for a third time in the match and secure progress. You know, today I was a little bit lucky.
The 36-year-old Swiss extended his winning run on grass to 18 matches as he continues a serene build-up to his title defence at Wimbledon next month but after easing through the first set found Paire in one of his more inspired moods.