The result moved Houston atop Group 3 with seven points, three better than Olimpia, and eliminated Salvador's FAS from quarterfinal contention. Olimpia will play at FAS next week before Houston hosts the Honduran side in the group finale on October 23.
Twenty-four-year-old English midfielder Giles Barnes scored his first goal since being acquired by Houston last month and Clark served Bobby Boswell and Cam Weaver for later strikes. Calen Carr added a finale as Houston extended its unbeaten streak at home to 22 in competitive matches, 15 since it opened the $95 million BBVA Compass Stadium on May 12.
FAS, which has won only one of its last six, lost its fifth straight in the Champions League and has been outscored 10-1.
With Houston making nine changes to the lineup it started in Friday's 1-1 draw with Sporting KC in Major League Soccer, both sides generated only one shot apiece through the first 20 minutes. But Houston came alive when goalkeeper Tyler Deric's drive up field was headed down to Barnes, who dribbled in from the top of the defensive third and beat FAS keeper Daniel Arroyo with a left-footed drive inside the right post from 25 meters.
Barnes had played only nine minutes for Houston entering the match.
FAS was limited to chances from distance and Houston doubled its lead in the minute before halftime when Clark curled an in-swinging free kick from the right side into the six-yard line, where Boswell had a flick header into the far-side netting.
The Salvadoran side had possibly its best month just after the start of the second half when Ricardo Ulloa was able to get to an angled ball into the area, but his first touch was too heavy and Deric was able to grab.
Weaver virtually settled the match in the 49th when he attempted to head Clark's cross to Brian Ching in front of goal. Elder Figueroa was able to get a leg to intercept, but only tapped it back to Weaver inside the six and the 29-year-old American pounced to score his first goal the season.
Weaver also had an assist in the 78th, heading a high ball to Carr, who took a touch and chipped a sprawled Arroyo from the edge of the six.
It was fifth time in seven Champions League games without a goal for FAS, which has only one win in 11 matches in the competition.