Del Potro traded breaks with his third-seeded Bosnian opponent in the first two games of their Friday-night semi-final.
Fognini gave up an opening break and fell in a 3-0 hole but was almost flawless from there, starting with a streak of five consecutive games.
The 22-year-old was beaten 6-4 6-2 by the second seed and world number 15, having lost in the last four of the Atlanta Open last week.
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The pair exchanged two breaks each in a more closely-fought second set, before 21-year-old Boulter found some momentum and broke again to level the match and force a decider. He came back from a set down to beat Quentin Halys in three.
Central to del Potro's chances of success in this match, and any other, is how effectively he is able to bring his forehand into play. "I made some mistakes in the end of the set, but then I played a smart game in the tie-break".
Italian tennis player Fabio Fognini kisses his trophy as he poses for the media after winning against Argentinian Juan Martin del Potro (not pictured) during the final of the Los Cabos Tennis Open, in Baja California Sur, Mexico, 04 August 2018. Giron, ranked outside the top 300, gave a good account of himself but ultimately could not match del Potro's power, losing 5-7 3-6. "I took my chances to win and I'm glad to reach another final this season". "It was a good week for me", Del Potro said.
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