Sammy Ochoa and Eddie Johnson gave Seattle the lead twice, but penalties in each half by Mario Berrios equalized twice and had the match tied entering the final 20 minutes.
With its third win in as many games, Seattle - a quarterfinal loser to eventual finalist Santos in last season's Champions League, assured itself of the Group 4 title with one game remaining.
Seattle took a 1-0 lead in the 11th minute as Marc Burch exchanged passes with Mario Martinez, who whipped a cross into the penalty area where Ochoa bounced a header inside the near post from seven meters. It was the third straight Champions League match that Ochoa has scored a goal.
Alex Caskey had a chance to double the advantage in the 16th minute, but Marathon keeper Jose Mendoza parried away the deep cross before Luis Castro headed clear of danger.
Seattle thought it had a two-goal lead in the 30th minute, but Scott was whistled for a foul for clattering Mendoza on a 50-50 ball.
Three minutes after his chip from 14 meters went just over the bar, Berrios equalized for Marathon in the 35th minute, beating Michael Gspurning from the penalty spot after the keeper tripped Mitchel Brown.
Buoyed by the equalizer, the Hondurans attacked with more zest, but Randy Diamond's attempt in the 41st minute was parried away by Gspurning, who also denied Julian Rapalo from the top of the box two minutes later.
The visitors reclaimed the lead in the 61st minute when Johnson took a pass from Andy Rose off his chest and the U.S. international fired a volley past Mendoza.
But Salvadoran referee Marlon Mejia called for Marathon's second penalty kick of the game in the 67th minute, ruling Patrick Ianni tripped Rapalo inside the box. Berrios again stepped to the spot and this time pulled Gspurning the wrong way for the 68th-minute equalizer.
Ten minutes later Evans powerfully headed Osvaldo Alonso's right-sided cross inside the far post from 12 meters to put Seattle in front, 3-2.
Marathon wraps up group play against Caledonia September 26 in San Pedro Sula, while Seattle faces Marathon at CenturyLink Field on October 24.