With the Giants down by seven and having just given up a touchdown, Eli looked for Mario Manningham over the middle and the pass was intercepted by Carlos Rogers.
On the next play, Kendall Hunter went 17 yards into the end zone.
Honestly, it's hard to pin the interception only on Eli, considering Manningham clearly stopped at the top of his route when he shouldn't have. The result made Eli look like he was throwing to nobody.
The 14-point deficit proved too much to overcome, though the Giants scored and eventually drove inside the 10-yard line with a chance to tie the game. Justin Smith knocked down a 4th and 2 pass from Eli to Victor Cruz and the game was over.
There is no worse way to lose a game (on a non-scoring play) than a tipped ball at the line of scrimmage.
Here are five things that we learned from this devastating loss.
If there was any game for the Giants to show that their run defense was going to be worthwhile down the stretch, this was definitely it.
Frank Gore was held to 0 yards on six carries in the first half and didn't touch the ball in the second. Overall, the 49ers ran the ball 20 times for 77 yards, which was by far the best showing by the Giants' run defense in the last month and a half.
OK, so while the run did work occasionally for the Giants today, it was generally a bad day running the football and it ultimately cost them key opportunities late.
Kevin Gilbride went into his shotgun draw mode that all Giants fans hate; he ran that far too often in the fourth quarter and on the final drive.
When you're down by seven trying to mount a comeback, you can't handicap your offense with one- and two-yard draw plays.
The biggest blunder was on 3rd and 2 from the 10-yard line at the end of the game. Instead of putting the ball in Eli's hands after he'd been making play after play, "Killdrive" wastes a play and calls a draw that gets stuffed.
Granted, the play had been getting five yards every now and then, but that wasn't the time to get cute. Eli had already converted two fourth downs, and Killdrive was playing with fire to expect a third if Ware didn't convert.
When you're going against the league's best rushing defense, you don't run the ball in crunch time.
One thing you can say about this 2011 Giants team is there is absolutely no quit in them. I bet if you asked them what quit meant, they'd shrug their shoulders.
After that horrible sequence of events that saw the 49ers score 15 points in 61 seconds, the Giants easily could have folded.
Instead, they again rallied around their quarterback, who nearly led them on an improbable comeback. Were it not for a Justin Smith tip and some poor play-calling by Gilbride, we might have been talking about a game that went to overtime.
As much as it pains to say it, special teams played a huge factor in the outcome of this game.
In the first half, the 49ers were kicking off with five minutes to go when they attempted and recovered an onside kick. It was a big swing in momentum that led to a field goal.
Then in the fourth, Steve Weatherford shanked a 29-yard punt that set the 49ers up at midfield—on the ensuing drive they took the lead on a Vernon Davis 32-yard catch and run.
The Giants had been playing great on special teams this year, but these two plays were a big difference.
Despite losing a game advantage and now only holding a one-game lead in the division over the Cowboys, life is good for the Giants moving forward.
The Giants still have a very tough road ahead, but they have to be feeling good about their chances.