The LaLiga champions, who were knocked out at Anfield after letting slip a three-goal advantage from the first leg, seemed to still be struggling in the aftermath against opponents aiming for a top-four finish.
Arturo Vidal capitalised on one of the few opportunities Barca carved out in a game played at a leisurely pace, with Ernesto Valverde's men in no mood to over-exert themselves having wrapped up the title two weeks earlier.
Getafe had threatened to heap further misery on Barca before falling behind; Jorge Molina blazed a golden chance over the crossbar early on and while he did find the net after 25 minutes, his effort was ruled out for offside.
Barcelona created little in the final third before Ivan Rakitic had a first-time shot saved by David Soria, who could then only parry Gerard Pique's glancing header, allowing Vidal to pounce on the rebound.
Malcom should have made it two when he arrived unmarked in the penalty area but Soria saved his effort to keep the deficit down to one at the break.
The Brazilian forward missed another opportunity early in the second half, failing to convert from point-blank range after Pique's shot had bounced back into his path.
Molina hit the post as Getafe went agonisingly close to equalising before Messi powered his way into the box in the 89th minute, forcing Dakonam into a desperate sliding challenge that only deflected the ball against team-mate Arambarri and into the net.
What does it mean? Fourth place out of Getafe's hands
Getafe go into the final day of the season level on points with fourth-placed Valencia, who have the edge in the head-to-head record between the two sides.
Impressive Coutinho limps out
While he has found it tough going at Barca this season, Philippe Coutinho was the focal point for some of his side's best play before a knock saw him substituted midway through the second half.
Barcelona were way short of their best but Getafe goalkeeper Soria struggled to deal with their few shots on target. He was also made to pay for his failure to hold Pique's header, inadvertently setting up Vidal's opener.
Key Opta facts
- Arturo Vidal has been directly involved in nine goals in LaLiga this season (three scored and six assisted), more than any other Barca midfielder.
- Barcelona have lost just two of their 28 LaLiga games against Getafe (W20 D6), fewer than against any other side they have faced that many times in the competition.
- Ernesto Valverde has won 15 of his 19 LaLiga games against Getafe (D1 L3), more than against any other opponent in his managerial career.
- Getafe failed to register a single shot on target in a LaLiga game for the first time this season.
- Barca have won their last seven LaLiga matches at Camp Nou, their best run at home under Valverde in the competition
Getafe will hope to force their way back into the Champions League places when they take on Villarreal at home, while Barcelona travel to Eibar on the last day before their Copa del Rey final against Valencia.