Honduras faced a stiff challenge from Costa Rica, making its first appearance of the tournament, before the Catrachos pulled away late for their second straight win on the strength of a hat-trick from Alberth Elis.
In the late game, host Guatemala got a hat-trick of its own to also gain an inside track towards qualifying for the finals of the 2013 CONCACAF Under-17 Championship in Panama.
El Salvador played the Guatemalans evenly through much of the game, but the locals rode Christopher Ortiz's three-goal performance to victory, giving the Guatemalans four points and the provisional second place.
Ortiz opened the scoring in the 28th minute, taking advantage of a loose ball in the area to get off a shot, and then netting his own rebound to break a scoring drought for the host, who was shutout by Nicaragua on Friday.
The standout Guatemalan forward scored again seven minutes after the interval to double the lead, this time on a splendid free kick from just outside the Salvadoran area.
A determined El Salvador side refused to give up, and cut into the lead in the 57th minute via defender Juan Barahona, who sliced home a cross.
Just six minutes later Guatemala was down to ten men, as Rafael Arriaga was sent off with a double yellow. Salvadoran Jose Contreras then saw straight red six minutes later, leaving the teams again level.
The score was then leveled as well on 73 minutes, when Oscar Hernandez headed in a corner, setting up a dramatic conclusion.
With just minutes remaining, Ortiz was fouled in the box, and stepped up to deposit the resulting spot kick to give the host a valuable 3-2 win, which puts them close to qualifying for the confederation championships.
"We're just glad to get the win and get on track," said Ortiz. "Now we'll come back in the next match against Honduras, and we're going for first place."
In the early game, early tournament leader Honduras had its hands full with a determined Costa Rica side, in action for the first time in Guatemala after a first match day bye.
The Ticos looked lively on the ball under the hot midday sun, and nearly opened the scoring several times, including early in the second half, when defender Elmer Guity flashed a corner kick just high of the Honduran crossbar.
Betting on its speed and the counterattack, Honduras instead broke through in the 51st minute, as speedy target man Alberth Elis raced onto a long pass and finished past Costa Rican goalkeeper Jorge Jara.
Down a goal, the Ticos continued to press, but their efforts to tie the match were severely hampered by a red card to Andrey Mora midway through the half.
Honduras eased to an eventual 3-0 victory from there, as Elis scored a second on a quick counter in the 72nd minute, before finishing another break, and his impressive hat-trick, six minutes later, to leave the Catrachos atop the group after two rounds with a perfect six points.
"We're happy to get another win," said midfielder Brayan Velasquez, the provider on two of Elis's goals on the day. "It puts us in good position, but nothing is settled yet. Our goal is to come out on top every game."
The next round takes place on Tuesday, when Honduras can clinch a spot in the regional finals with a win against Nicaragua. Costa Rica and El Salvador then face off in the late match, both looking for their first win of the tournament.