Fraile (Astana) finished ahead of mountains classification leader Julian Alaphilippe (Quick-Step Floors) and Jasper Stuyven (Trek-Segafredo) at the end of a challenging 188 kilometres from Saint-Paul-Trois-Châteaux to Mende.
Fraile claimed his second win of his Grand Tour career, matching his efforts in last year's edition of the Giro d'Italia, where he claimed victory on another medium mountains stage.
"It is amazing, absolutely incredible," said Fraile. "I can’t believe it! For me it was a dream to win a stage at the Tour de France. And now this dream came true.
"Last year I won a stage at the Giro and now I repeat my success at the Tour. Already yesterday I felt quite good and today I was motivated to go in a breakaway, to try to fight for the stage. I knew it would be difficult, especially because the group was really big."
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The peloton was content to let the break have its day and arrived at the finish 20 minutes after Fraile had claimed the stage. Primoz Roglic (LottoNL-Jumbo) clawed back a handful of seconds with an impressive attack, although all the other contenders ended up conceding more time to the top three of Geraint Thomas, Chris Froome (both Team Sky) and Tom Dumoulin (Team Sunweb).
It was a windy start to Stage 14 with the peloton almost immediately splitting up into four separate echelons as it passed through the Rhone valley.
But it soon settled into two groups with the break made up of over 32 riders including the leader of the points classification Peter Sagan (BORA-hansgrohe) and Julian Alaphilippe (Quick-Step Floors) in the Polka Dots of the mountains classification.
Unsurprisingly the stage winner would come out of that group but not before with Sagan added to his considerable points lead at the Besseges intermediate sprint and Alaphilippe the KOM points at the Cote du Grand Chataignier.
With Sky setting the tempo and the break settled in, the situation remained the same until Gorka Izagirre (Bahrain Merida) slipped away from the break in an attempt to win from 62km out and taking the maximum points on the Col de la Croix de Berthel.
Tom-Jelte Slagter (Dimension Data) and Jasper Stuyven (Trek-Segafredo) bridged across to make it a trio of riders, the larger break and peloton separated by some 15 minutes.
With less than 40km to go the larger group of chasers split to pieces on a surprisingly hard gradient with Alaphilippe leading the charge along with Fraile.
Stuyven then committed to pressing on without the help of Izagirre and Slagter with 35 kilometres remaining. That was the way it rolled until the final kilometres on the steep ascent to Mende when Fraile, chasing desperately, succeeded in bridging to the lone leader.
