Jamaica (2-0-1) had been on the defensive for much of the game against a hard-charging El Salvador side. But McCleary ended the deadlock when he knocked in a rebound after a diving save by Derby Carrillo on a Joel McAnuff shot sent the ball his way.
McCleary, who plays for Reading in England, has made his presence felt in the tournament. His cross set up the winning goal in stoppage time by Rodolph Austin in Jamaica's 1-0 win over Canada on Saturday in Houston.
The Jamaicans, who finished atop Group B, will play their next game without Vancouver Whitecaps forward Darren Mattocks who was sent off in the 80th minute for a second yellow card.
The result all but eliminated El Salvador (0-1-2), with the official chop coming via the later Canada-Costa Rica game or possibly the final round of games in Group C.
The top two teams in each of the three groups plus the two best third-place teams move into the knockout round of the CONCACAF championship, which covers North and Central America and the Caribbean.
Jamaica is ranked 76th in the world by FIFA, compared to No. 88 for El Salvador. But the Central Americans had the best of the game for the last hour.
It was a chippy contest and Guatemala referee Walter Lopez had his hands full.
Jamaica was forced to make two injury-related substitutions before the midway point of the first half at BMO Field on a sunny evening as defender Jermaine Taylor, in the eighth minute, and goalkeeper Dwayne Miller, in the 22nd, were both stretchered off.
Jamaica came close to scoring in the 20th minute when Carrillo spilled the ball after saving a free kick. A Jamaican got to the ball, beat the byline, but his sharply angled shot was just wide.
The close call seemed to spur El Salvador on and the Central Americans pressed the rest of the half. Replacement Jamaica goalie Ryan Thompson had to punch away a Richard Menjivar free kick from the side of the box in first-half stoppage time.
Thompson had to make a double save in the 58th minute, parrying away a long-distance rocket and then stopping a shot off the rebound.
El Salvador's Arturo Alvarez shot just wide in the 72nd minute.
Jamaica's MLS strike force of Mattocks and Giles Barnes got little service throughout the game.
Earlier in the tournament, El Salvador tied Canada 0-0 and Costa Rica 1-1. Prior to beating Canada, Jamaica tied Costa Rica 2-2.
It's been a hectic schedule. The teams opened play last Wednesday in Carson, Calif. travelled to Houston for games Saturday and then Toronto.
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