It was Atlanta's second goal scored past the 85th minute in as many games. Marcelino Moreno won United's previous match deep in second-half stoppage time at home against Montreal.
Raul Ruidiaz scored his team-leading sixth goal in the sixth minute for Seattle (5-0-2, 17 points), which still completed its best seven-match start to an MLS season.
Neither side had much in the way of chances, with each recording only two shots on target. Atlanta (2-1-3, 9 points), however, continued its trend of dominating possession in all its matches by holding 63 percent of it.
The Sounders still have not conceded a goal from open play, but they also required a set piece to score when Ruidiaz gave his side the early lead.
Atlanta United were probably more dangerous in the first half than the second, but they were rewarded for their continued effort when Lennon bombed forward from his fullback spot.
As Lennon dragged his cross back toward the penalty spot from near the goal line, Smith slid to try and block it, but was late and contacted Lennon instead.
Referee Kevin Stott pointed toward the penalty spot. Martinez took the kick, driving it into the top right corner for his 79th career MLS goal, the most in Atlanta history.