Fernando Santos' Brazil-bound side had not scored in their past three international appearances, but were aggressive from the opening minute at the Red Bull Arena.
Panagiotis Kone powered a header past Bolivia custodian Romel Quinonez, running into the area to get on the end of a chipped cross in from Dimitris Salpingidis in the 21st minute.
Kostas Katsouranis' classy finish on 54 minutes gave Greece some breathing space, as his glancing header from a Jose Holebas corner found the top-right corner.
Bolivia pulled a goal back via a 35-yard strike from Rudy Cardozo that was bundled into the net by Greece goalkeeper Orestis Karnezis with 20 minutes to play.
But Greece held on for their first win in five matches, a necessary boost for Santos' men ahead of the FIFA World Cup.
Greece pressed hard on their Bolivian opponents from the outset, and it almost resulted in an early howler from the South American nation.
A Bolivia back-pass was chased down by Greek forward Theofanis Gekas, who forced goalkeeper Quinonez into a panicked clearance in the fourth minute.
Gekas was again in the thick of the action as he missed a shot from point-blank range eight minutes later.
The Konyaspor front man took a touch from a cross in from Georgios Samaras, but his blind turn on goal saw him hook his shot wide despite a lack of pressure from the Bolivia defence.
Greece would eventually convert their dominance when Kone buried his free header - their first goal in 357 minutes.
Bolivia began to hunt an equaliser but failed to put their opponents under any serious pressure, despite earning multiple corners.
The best chance of the half for Xabier Azkargorta's men fell to Alejandro Melean, but his header from Gualberto Mojica's corner on 34 minutes was well high and wide of the target.
Both sides were attacking early in the second half, with the two goalkeepers called upon inside the opening four minutes after the restart.
And Greece doubled their advantage in the 54th minute from a set-piece, as Katsouranis converted from Holebas' corner.
Moments earlier, Gekas had the chance to capitalise on a Bolivia turnover.
Samaras forced the turnover, and their charge up the field ended with the veteran forward sliding in at the far post, but he failed to control his effort, spraying it well wide of the Bolivia goal.
Marcelo Moreno could have got Bolivia back into the contest when he was one-on-one with Greece custodian Karnezis, but he punched his shot wide right.
Gekas' fortune in front of goal did not improve, as he was one-on-one with Quinonez moments later after being played through by Giorgos Karagounis – however, he was denied by the onrushing goalkeeper.
Bolivia's fortunes were on the rise, however, as Karnezis saw plenty of Cardozo's strike, but clumsily saw it come off his hands and into his own net.
It was the first goal Greece had conceded in 285 minutes, but they never looked likely to concede a second.
Greece begin their World Cup Group C campaign against Colombia on June 14, before fixtures against Japan and Ivory Coast.
