Dallas' unbeaten start to the MLS season was ended, while the Houston Dynamo were thrashed on Saturday.
An 81st-minute goal from Jahmir Hyka saw the San Jose Earthquakes to a 1-0 win which marked Dallas' first defeat.
Hyka's goal was a stunner as he jumped to take a touch over a defender before calmly placing a finish in off the post.
Dallas' loss – the first Oscar Pareja's men have suffered through 10 games – left them third in a Western Conference which saw its top three teams beaten.
Second-placed Houston was no match for Miguel Almiron and Atlanta United, who recorded a 4-1 win.
Almiron opened the scoring for the home side on the half-hour mark, taking a touch before unleashing a powerful left-footed effort past Joe Willis.
He doubled his and his team's tally before halftime, skipping into the area before making it 2-0.
Julian Gressel extended the lead in scrappy fashion before Almiron completed his hat-trick from the penalty spot.
Erick Torres scored a late penalty for Houston, whose second straight loss left the club second in the table.
Sporting Kansas City remains top despite suffering a 2-0 loss away to the Vancouver Whitecaps.
The Chicago Fire continued their climb up the Eastern Conference table, extending their winning streak to three and moving into second after a 1-0 success against DC United.
The Montreal Impact moved off the bottom with a 4-1 thrashing of a 10-man Portland Timbers side, while the Seattle Sounders edged Real Salt Lake 1-0 to stop their slide.
The Philadelphia Union stretched their winning run to four games with a 2-1 victory over the Colorado Rapids, who had a man sent off.