The Uruguayans took the lead in the Group D clash thanks to a disputed Edinson Cavani penalty midway through the first half before the Central Americans turned the match on its head after the break.
Young striker Joel Campbell chested down a cross from the right and slammed a low shot past keeper Fernando Muslera after 54 minutes.
Then centre back Oscar Duarte gave Costa Rica the lead in the 57th minute with a brave diving header at the back post from a Christian Bolanos free kick.
Marco Urena completed the remarkable victory with a third in the 84th minute, silencing an army of sky blue-clad Uruguayan fans in Fortaleza's Castelao arena.
Uruguay's misery was compounded in stoppage time when their defender Maxi Pereira became the first man to be sent off at this World Cup.
It had all looked so different in the first half when Diego Lugano went down in the box under pressure from Costa Rica defender Junior Diaz as he tried to get on the end of a Diego Forlan free kick.
Diaz clearly had his arms around the waist of his opponent but even so the Uruguayan captain made a meal of the challenge.
Nevertheless, German referee Felix Brych pointed to the spot and Cavani slammed home the penalty.
Uruguay face England in their next group match while the jubilant Costa Ricans, who have only once made it out of the group stages at a World Cup, will take on Italy.
Image: Joel Campbell celebrates with teammates after scoring
Photograph: Mike Blake/Reuters