Debutant Federico Valverde produced some heroics, the 19-year-old's 76th-minute strike helping end Uruguay's six-match winless streak on Tuesday.
Luis Suarez and Edinson Cavani were isolated and largely ineffective as Uruguay struggled against the dominant Paraguayans in Asuncion.
Fernando Muslera kept Paraguay at bay in the second half and Uruguay went on to stun Paraguay, with Valverde's deflected long-range effort silencing the home crowd before Gustavo Gomez's own goal doubled the visitors' lead.
Angel Romero managed to pull a goal back in the 88th minute, setting up a tense finale, but Uruguay held on for a first World Cup qualifying away win in Paraguay as they moved above Colombia into second spot, while the hosts remain seventh after 16 matches.
Paraguay upstaged Chile 3-0 last week and the hosts made just one change to that team, with Romero coming in for Miguel Samudio.
There was a consecutive start for Uruguay star Suarez. The Barcelona forward hobbled off in the goalless draw at home to Argentina having surprisingly returned to action following a knee injury suffered in the Supercopa de Espana second-leg loss to Real Madrid on August 16.
Maximiliano Pereira and Valverde were the new faces in Oscar Tabarez's XI as Gaston Silva and Alvaro Gonzalez made way.
It was a full-blooded affair in Paraguay, with tackles flying in from all angles in the first half.
Overall, neither side created any real clear-cut opportunities, though Cavani beat the offside trap and fired a shot across goal and past the post in a rare foray forward for Uruguay.
It was one-way traffic in the second half as Paraguay dominated proceedings – Suarez and Cavani largely neutralised and isolated up front.
Uruguay goalkeeper Muslera was kept busy, on hand to deny Oscar Romero from close range with his legs six minutes after the interval.
Paraguay continued to pepper the Uruguay goal, this time Gomez narrowly heading over the crossbar just past the hour-mark.
Moments later Lucas Barrios almost broke the deadlock with a glancing header, but a scrambling Muslera managed to make a fingertip save.
Paraguay were unable to make their dominance count and it proved costly as Uruguay scored against the run of play – Valverde benefiting from a deflection to put the visitors ahead.
Pushing numbers forward in search of an equaliser, Paraguay were caught out at the back with 10 minutes remaining after Suarez rounded the keeper and while the chance appeared gone, his strike hit the crossbar and bounced off Gomez and fortuitously into the net.
Santiago Salcedo hit the post two minutes later before Paraguay team-mate Romero reduced the deficit, but it was too little too late.