Despite Bolivia being already eliminated at the bottom of the South American group, both sides were committed to attack in a sometimes sloppy match between two Andean nations played at nearly 4,000 metres above sea level.
The draw left Ecuador in fourth place in South American qualifying with 22 points as they seek a berth in the 2014 finals in Brazil.
Two minutes after coming on as a halftime substitute in his first international, 20-year-old Bolivian Jaime Arrascaita stunned the Ecuadoreans with a powerful shot that slipped through the hands of goalkeeper Alexander Dominguez.
Ecuador, though, received a boon 11 minutes later when Brazilian referee Paulo Cesar de Oliveira called a controversial penalty in their favour after Bolivia's captain Ronald Raldes touched the ball with his arm as he fell under a challenge.
Caicedo sent Bolivia's goalkeeper the wrong way and fired the ball into the corner of the net for his sixth goal in the qualifiers.
Ecuador, showing signs of fatigue after losing 1-0 to Colombia on Friday in a torrential downpour in Barranquilla, struggled against a feisty Bolivia at the Hernando Siles stadium.
Striker Jefferson Montero displayed deft footwork to get the ball into the net in the 14th minute but was ruled offside.
The top four teams in the nine-nation group at the end of the qualifying campaign next month will go through to Brazil, with the fifth-placed side taking on Jordan over a two-legged play-off for one more berth.