Wingers Ronaldo and Ecuador's Antonio Valencia scored one each in the first half of a match that treated fans at the Estadio D. Afonso Henriques in Guimaraes to a feast of attacking play and chances.
Ronaldo's goal, which levelled the score in the 23rd minute, came after he chased a backheel from Fabio Coentrao and unleashed a delightful volley.
Portugal pulled ahead in the second half through a Helder Postiga tap-in but just when the hosts looked on top Joao Pereira gifted Ecuador an own goal when he misjudged a backpass.
Caicedo compounded Portugal's woes by firing in to put Ecuador in front with 20 minutes to go.
The defeat means Portugal have failed to win their last four matches while Ecuador remain unbeaten in seven games as they enjoy a best-ever 12th place in the FIFA rankings, six places above 2014 World Cup hosts Brazil.
"We dominated for most of the match but lost a bit of fluidity at some point," Portugal coach Paulo Bento told Portuguese television. "We were unlucky not to keep our advantage. I think we had a good match despite the mistakes."
Portugal, who are third in World Cup qualifying Group F, will hope to have learnt from their errors by the time they play their next qualifiers in March.
"Regardless of the result we were always going to be under pressure when we play the qualifiers against Israel and Azerbaijan next month," added Bento, whose team are level on seven points from four games with second-placed Israel and five adrift of group leaders Russia.
Valencia punished some lax defending from Portugal early on with a header but Ronaldo, who turned 28 on Tuesday, equalised with a sweet volley after a series of first-time touches from his team-mates.
Postiga put Portugal ahead in the second half after some flowing play between Ronaldo and Nani and Portugal looked to be in control.
But moments later right-back Pereira horribly misjudged a backpass to goalkeeper Eduardo and looked on in despair as the ball slowly drifted into his own net.
With Portugal's back four shaken, Caicedo grabbed a memorable winner from outside the box, connecting with a first-time shot from a Christian Benitez chested ball.
Portugal substitute Silvestre Varela hit the bar late on and Ecuador forward Benitez missed a sitter in stoppage time but he will not have been kicking himself too much after an impressive display by the South Americans.
