Monfils beat another German, Florian Mayer, 6-3 6-2.
Top seed Nadal was far from his best but said he was pleased with the way he responded to falling behind against a player enjoying the best week of his career.
"The positive thing is I am in the finals the first week of the season without arriving here with big preparation," Nadal was quoted as saying on the ATP Tour website (www.atpworldtour.com)
"Without playing my best, I was able to find a solution. It's true that I finished the match playing better than what I started. That's always a positive thing."
Gojowczyk, 24, won the first nine points of the match and held his nerve to claim the opening set.
Nadal responded to open a 4-0 lead in the second set but his opponent refused to fade away and briefly threatened at the start of the decider before succumbing.
Injury-plagued Monfils, who has not won a title since 2011, has lost eight of his 10 matches against Nadal but will feel confident after a commanding performance against Mayer.
The 2012 Doha runner-up needed only 55 minutes to win his semi-final, sending down nine aces.
(Writing by Martyn Herman in London; editing by Ken Ferris)
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