While the Barcelona star was initially named in head coach Edgardo Bauza's eleven, a late suspension imposed by FIFA just prior to the match ruled him out, adding to an already depleted Argentina side who were already without Nicolas Otamendi, Lucas Biglia, Javier Mascherano and Gonzalo Higuain.
Playing at an altitude of 3,600 metres, Bolivia took full advantage as they went ahead just after the half-hour mark with Juan Carlos Arce steering a header past Sergio Romero while Marcelo Martins doubled the lead in the second half with a thunderous strike.
Argentina's failed to mount a comeback as their struggles against the hosts continued, having not won in Bolivia since 2005, while their woeful record without Messi during the campaign now stands at one win in eight matches.
Perhaps buoyed by the opposing captain's absence Bolivia came out with an attacking mindset, with Pablo Escobar, Martins and Arce all coming close as Mauricio Soria's side piled on the pressure and limited Argentina to ineffectual counter-attacks, taking the lead when Arce beat Roncaglia to Escobar's delivery to head the ball past Romero.
Ramiro Funes Mori was forced off with an injury before the half-time break, with Argentina's woes extended after the restart when Martins slammed home the ball after being left unmarked at the back post, latching onto a Jorge Flores ball.
Edgardo Bauza responded by sending on Sergio Aguero but Argentina failed to mount a comeback, with substitute Marcos Acuna forcing Carlos Lampe into a save as the visitors tried to salvage something from the game withtheir grip on automatic qualification becoming more difficult as the match ended 2-0.
