The Crew, which rested Guillermo Barros Schelotto, Alejandro Moreno and four other starters from its 2-1 win over Houston on Sunday, stunned Saprissa with an Eddie Gaven goal in the fifth minute and staved off the Ticos the rest of the game.
With two wins and six points in three games, Columbus is a point behind group leader Cruz Azul, which it hosts next week. Saprissa remained in third with three points, and Puerto Rico Islanders of USL-1 are last with one point.
Columbus scored with a string of passes that covered three-quarters of the field, with Jason Garey and Brian Carroll springing Gaven from midfield. Gaven shook off a challenge by defender Andres Nunez to control the bouncing ball and rolled it past keeper Keilor Navas a yard inside the far post.
Walter Centeno headed home from an offside position midway through the first half, Duncan Oughton cleared a shot off the line a few minutes later, and two minutes before halftime keeper Will Hesmer tipped away a shot bound for the top corner. Hesmer saved again early in the second half when he covered a shot by Jairo Arrieta, and Saprissa fluffed a great chance for an equalizer late in regulation when Olman Vargas got free just outside the goal area but shot wide.
Sept. 16 in San Jose
Saprissa 0, Columbus Crew 1. Goal: Gaven 5.
Saprissa - Navas, Drummond, Cordero (Santana, 76), Nunez (Russell, 86), Loaiza, Centeno, Sequeira, Barrantes, Alonso, Arrieta, Elizondo (Vargas, 62).
Columbus - Hesmer, Zayner, O'Rourke, Iro, Ekpo, Moffat, Carroll, Gaven, Oughton, Garey (Rogers, 60), Lenhart.
Referee: Roberto Garcia Orozco (Mexico).