Supporters' Shield leader Atlanta struck three times in the final 20 minutes to edge past the Earthquakes 4-3.
Nick Lima headed in a Shea Salinas cross for the Earthquakes' opener at Avaya Stadium.
Danny Hoesen doubled the lead before half-time for San Jose, which is struggling at the bottom of the Western Conference.
But Gerardo Martino's Atlanta struck prior to the break, Hector Villalba's wonderful curling effort from 25 yards dragging United back into the game.
The Earthquakes restored their two-goal lead through Valeri Qazaishvili, whose fine individual effort made it 3-1 in the 58th minute.
San Jose thought it had taken a 4-1 lead through Chris Wondolowski, only for his strike to be ruled out by the video assistant referee (VAR) and a penalty awarded to Atlanta.
Josef Martinez converted the spot-kick and the visitor was level just three minutes later, Miguel Almiron drawing it level.
There was late drama, Martinez heading in an Almiron cross in the 95th minute to complete Atlanta's comeback.
Atlanta moved four points clear atop the Eastern Conference, with New York Red Bulls in second.
Timbers moved into fourth in the Western Conference after a 3-2 win over Columbus Crew.
David Guzman cancelled out Niko Hansen's opener before an Andy Polo goal gave Portland the lead.
A Lalas Abubakar own goal early in the second half gave the Timbers a cushion, and they needed it after Hansen completed his brace late on.
In Seattle, the Sounders conceded late to go down to the 10-man Philadelphia Union 1-0 – ending their nine-game winning streak.