For the second time this season, Jack McInerney scored in second-half stoppage-time to break Toronto FC hearts and earn the Union a tie.
Nelsen was more interested in what had gone on before the Philadelphia goal Saturday. The Toronto manager branded defender Doneil Henry's ejection in the 41st minute for a second yellow card a "ridiculously soft sending-off."
"And we still looked really good," Nelsen said. "I'm really proud of the guys. The work ethic they put in and the determination. We still looked good when we had the ball. I can't fault the players. They were absolutely fantastic ... They worked really hard, they're gutted. They're absolutely gutted in there."
Still, once again a tie felt like a loss for Toronto (1-7-5) which is only three points better than it was at the same time last season (1-10-2) when it posted a league-record 0-9 start.
Toronto ended last season on a 14-game winless streak. Thirteen games into this season, it is mired in an 11-game winless stretch.
And a big reason why is Toronto has lost 11 points in seven games this season due to last-minute goals. Four of those have come in stoppage time and six have come after the 85th minute.
Nelsen, who insisted his team had no problem "11 vs. 11" on the day, was more than likely looking to take the heat off his players as he turned his attention on the officiating.
But however you rate referee Geoff Gamble's handling of the game — and several Toronto FC players had no complaint with Henry's two yellows — Toronto was the architect of its own demise by failing to put the game away in the first half.
The home side dominated the first 45 minutes but couldn't convert that into goals or chances. Toronto earned six corners in the first half but put only one shot on net.
Toronto striker Danny Koevermans, who made his comeback from knee surgery as a substitute late in the game, had no complaints with the officiating.
"Is the referee to blame today? No," the straight-shooting Dutchman said of Gamble, who was working his 22nd career MLS game. "He did what he had to do."
Rookie midfielder Jonathan Osorio's goal in the 66th minute had looked like it might be the winner for struggling Toronto.
New Zealand substitute Jeremy Brockie made the goal with a fine swerving cross from the right flank. The 21-year-old Osorio, who won his first cap for Canada earlier in the week, flung himself at the ball and scored with a flying header.
It was the third goal of the season for the native of Brampton, Ont., who earned his second start after a fine showing off the bench last week in New England.
The tying goal came just as regulation time wound down, prompting a groan along press row from a group of reporters who have seen no shortage of late goals leaked by Toronto.
A long throw in by Sheanon Williams was headed away by Toronto's Jeremy Hall but only as far as McInerney, whose low shot through traffic beat Joe Bendik as three defenders rushed at the shooter.
One can wonder how a defence could leave McInerney alone, given he entered the game tied for the lead in league scoring with nine goals.
McInerney also scored in the 94rd minute on April 13 to earn Philadelphia a 1-1 tie with Toronto when the teams met at PPL Park.
The young striker, named MLS Player of the Month in April and May, came into the game leading the league with five game-winning goals.
The contest was an ill-tempered affair with plenty of shoving and three yellow cards for each side.
Philadelphia goalie Zac MacMath and Henry were both yellow-carded in the 27th minute after a shoving match that saw MacMath object to Henry getting in his way while trying to kick the ball away.
Hall said Toronto's strategy was to get into MacMath's face.
"We'd seen the tape from previous games .. we thought if we can put him under pressure and get into his head a little mentally, we'd be all right. And that's what we did."
Nelsen accused MacMath of assaulting his player, but said he was let off the hook by an inexperienced referee. "That's a sending off," he said.
"We always seem to get the inexperienced referees," he said. "That's life. Someone's going to have them. But they keep making inexperienced decisions. And we seem to be on the end of them."
Henry was sent off when he scythed down Danny Cruz on the edge of the box 14 minutes later. It seemed a clear foul by a defender clearly beaten on the play.
Koevermans said the linesman made the case to the referee for the second yellow.
"I think it was a good call, it was the correct call," he said. "It was a yellow card."
Koevermans was introduced for Toronto in the 86th minute, returning after more than 10 months out due to knee surgery. Nelsen said he made the move, taking off Brockie, to have fresh legs up front and help stop the Union from firing the ball back into their end after clearances.
"It's a happy day and a sad day," Koevermans said of his comeback, referring to the late goal.
Philadelphia (5-5-4) came into the game having lost two of its last three league outings, conceding five goals to Montreal and four to Los Angeles in the losses.
The game drew an announced crowd of 19,221, short of a sellout on a hot, humid and occasionally rainy evening. The venue is expected to be full Sunday for the women's friendly between Canada and the U.S.
Toronto has next weekend off before travelling to face league doormat D.C. United (1-9-2 ahead of Sunday's match with Chicago).
Toronto's only win this season was March 9 at Rogers Centre, a 2-1 victory over Sporting Kansas City.