Their loss extinguished the Quakes' minute playoff hopes and ended a four-game unbeaten streak for the last-place team in the Western Conference (7-13-7, 28 points).
Cunningham tallied his league-high 17th goal of the season in the 81st minute to decide the match, after he'd set up Ferreira to open the scoring early in the second half and Quincy Amerikwa equalized with his first MLS goal.
Missing midfield regulars Simon Elliott, Ramon Sanchez and Arturo Alvarez to international duty, the Quakes scrambled to cover spaces opened up by Cunningham's runs and the sharp passing of Ferreira, Dax McCarty and Dave van den Bergh. FCD ran the show for the first 20 or 25 minutes but its failure to score, thanks to a goalmouth clearance by Brandon McDonald and a Joe Cannon save, encouraged San Jose to gain traction in midfield. The first half ended in a 0-0 stalemate.
FCD broke through in the 49th minute, when Cunningham played Ferreira into space on the right flank and he drilled a shot past Cannon for his eighth goal. San Jose battled its way back into the match despite a dubious offside decision that deprived Ryan Johnson of a chance and an apparent handball that wasn't called.
The Quakes fired shots repelled by FCD keeper Dario Sala before and after substitute Amerikwa ran onto a through ball and coolly chipped a shot over Sala to tie the game. Just seconds after Johnson was called for a foul when he burst between defenders Heath Pearce and George John in the Dallas penalty area, Dallas countered quickly. McCarty ran onto a through ball that split open the Quakes' back line and he set up Cunningham to score into an empty net.
Cannon came up for a corner kick in stoppage time and nearly scored, getting his head to a bouncing ball that Sala deflected and Jair Benitez headed clear in a furious goalmouth melee. FCD held on long enough to assure that its Oct. 17 home game with Colorado, seventh in the overall standings with 40 points, will entail playoff implications for both teams.
San Jose, which in the past few weeks has dented the postseason prospects of Colorado and D.C. United, embraces another spoiler assignment when it plays at Toronto (11th overall) Saturday.
Oct. 7 in Santa Clara, Calif.
San Jose 1, FC Dallas 2.
Goals: Amerikwa (Salinas, Wondolowski) 73; Ferreira (Cunningham, Pearce) 49, Cunningham (McCarty, Ferreira) 81.
San Jose - Cannon, Leitch, McDonald, Burling, Zaher (Glen, 88), Salinas, Ribeiro (Amerikwa, 62), Corrales, Convey, Johnson, Wondolowski.
FC Dallas - Sala, Pearce, Ihemelu, John, Benitez, Chavez (Avila, 65), Hernandez, McCarty, van den Bergh (Wagner, 80), Ferreira, Cunningham (Shea, 88).
Referee: Hilario Grajeda.
MLS PLAYOFF STANDINGS
1. Columbus* (46 points)
2. Houston* (44)
3. Los Angeles* (44)
4. Chicago (41)
5. Seattle (41)
6. Chivas USA (41)
7. Colorado (40)
8. New England (38)
9. D.C. United (36)
9. Dallas (36)
11. Toronto (35)
12. Real Salt Lake (34)
13. Kansas City (32)
14. San Jose (28)
15. New York (18)
*clinched playoff spot