Rodriguez leads Bora's Russian climber Aleksandr Vlasov by seven seconds ahead of the final stage over rolling terrain on Sunday. German rookie Florian Lipowitz is third at 9sec.
Overnight leader Juan Ayuso of UAE could no longer keep up on the 14km final ascent when Egan Bernal put the hammer down for Ineos as the Colombian former Tour and Giro winner looked back to his best form.
EF rider Carapaz hi-jacked the Ineos plan when he tucked in behind their train on the six per cent gradient before accelerating away, 2km from home.
"I took advantage of the Ineos attack and I gave it all from there," said Carapaz, winner of the Olympic road race at the Tokyo Games.
A delighted Lipowitz of Bora was a surprise second as he outlasted teammate Vlasov while Bernal piloted Rodriguez to third on the day and the overall lead.
