The result improved the Costa Rican side to seven points in Group 6, two better than Tigres UANL, but with a match to play in Mexico on October 24.
Alajuelense had most of the possession and even a shot off the post before Sanchez converted the penalty in the 49th minute, created when Eliud Zeledon hauled down Anderson Andrade on the right edge of the area as the two wrestled for position for a bouncing ball.
The victory kept Alajuelense unbeaten at home in six Champions League matches while Esteli remained winless in eight games in the confederation championship, losing for the sixth time.
Alajuelense took the initiative from the start, getting its first solid chance in the 19th minute when Pablo Gabas headed Sanchez's corner kick, but clashed heads in a crowd inside the six and had to be carried off on a stretcher. He returned several minutes later.
Gabas put a header wide of the right post in the 25th minute from a Allen Guevara free kick, who had Liga's best chance just before halftime. Guevara's drive into the penalty area was blocked, but the ball fell to Gabas, who sent Guevera down the left side of the box.
Guevara turned toward the goal and unleashed a drive that caromed off the near post and bounded away harmlessly.
Alajuelense had its appeal for a penalty less than two minutes into the second half ignored by referee Hector Rodriguez, but the Honduran pointed to the spot half a minute later when Zeledon dragged down Andrade with his arm over his shoulder.
The Costa Rican side continued to control the match to the end, outshooting the Nicaraguan club 15-4.