There was a bright note for the Scorpions at half-time though as owner Gordon Hartman announced that the team had raised $662,559.
In other exciting news from the match Major League Soccer officials attended the match to run the rule over San Antonio following glowing reviews from US Soccer after the US Women's Team match last week.
The city's chances of getting an MLS team have been brought up over the past week with MLS executives listing San Antonio in a list of probable MLS markets and a good showing of 7,702 will be a big help.
San Antonio got off to the perfect start as they opened the scoring just three minutes in after sustained attack from the kick-off allowed Dennis Chin to find Tomasz Zahorski who buried yet another goal.
That seemed to wake the Cosmos up and they had a solid period of chances but wayward shooting stopped them from finding an early equalizer.
It was domination from the Cosmos in terms of possession but for all their chances they just could not beat Jeremy Vuolo with Kyle Reynish routinely shooting well wide.
Jaavier Saavedra nearly doubled the Scorpions lead in the 28th minute after Stephen DeRoux released the veteran but he just could not control the ball, letting New York off the hook.
The Cosmos responded almost immediately and Pedro Mendes finally got a shot past Vuolo only to be denied by the crossbar.
Saavedra continued to look threatening and in the 32nd minute his cross for Borja Rubiato just missed the Brazilian as the Cosmos cleared the ball to safety keeping it 1-0 at the break.
The second half was a completely different story as the Cosmos managed to storm back in to the match and found an early equalizer in the half.
Marcos Senna was the man to find the equalizer as he got the ball inside the area as he hit a powerful shot just inside the area that left Vuolo with no chance.
Just two minutes later the comeback was complete as Diomar Diaz made a powerful run in to the box before cutting the ball for Stefan Dimitrov allowed him to hit a powerful and pin-point strike to put the champions-elect in front.
Sitting with one hand on the trophy and one foot in the Soccerbowl allowed the Cosmos to sit back and saw the Scorpions really go for the match as they went on the attack.
That saw a rather sedate match but it exploded in the 72nd minute as Walter Ramirez went down after a trip from Dane Murphy which saw Murphy earn a red card.
That left the Cosmos bench incensed and lead to the newly re-signed manager Giovanni Savarese being sent to the stands following his reaction along with two yellow cards for their players for dissent.
Despite the man disadvantage New York managed to hold on and claim the title and head to the 2013 Soccer Bowl.