We've seen the footage (if you haven't, it's above for your convenience), and it's pretty clear that Andrew Jacobson's mugging of Darren O'Dea in the box in the 86th minute was a missed penalty call. We can't say for certain what was in referee Ismail Elfath's mind when he saw (or maybe did not see) what was going on, but looking at the Laws of the Game, it seems to be a call missed.
In regards to how penalties are awarded, we go to Law 14 of the IFAB Rules of the Game, the section that governs penalties:
A penalty kick is awarded against a team that commits one of the ten offenses for which a direct free kick is awarded, inside its own penalty area and while the ball is in play.
And of course, you must be wondering what those ten offenses would be, right? For that, here is the wording from Law 12, which governs direct free kicks:
A direct free kick is awarded to the opposing team if a player commits any of the following seven offences in a manner considered by the referee to be careless, reckless or using excessive force:
- kicks or attempts to kick an opponent
- trips or attempts to trip an opponent
- jumps at an opponent
- charges an opponent
- strikes or attempts to strike an opponent
- pushes an opponent
- tackles an opponent
A direct free kick is also awarded to the opposing team if a player commits any of the following three offences:
- holds an opponent
- spits at an opponent
- handles the ball deliberately (except for the goalkeeper within his own penalty area.
Again, if you look closely at the replay, Jacobson's arms were all over O'Dea, possibly even tighter than a static-charged snuggie. The offense was in the box, and satisfies Law 12 for a direct free kick, so how in Elfath's mind did one plus one equal zero in this case here? Again, it does seem to appear all the officials were in prime position to witness the crime.
This isn't the first time that we've had penalty calls dismissed wrongfully, and likely won't be the last. If Darel Russell hadn't struck just before stoppage, this would have been yet another sore point between TFC fans and MLS referees. The simple fact that it happened, and could have made an impact on the result, only fosters more disdain for match officials -- if MLS wants fans to respect the officials, perhaps a good start would be to crack down on referees for making simple errors like this!