Konopka got a piece of Koevermans' original close-range effort but the ball rebounded to the big Dutchman and Konopka couldn't stop the follow-up.
"It probably could have bounced anywhere off my leg but it bounced right back to him and he was able to get the rebound back," said Konopka.
"It's frustrating on that too in that we come up with a bit of a save and really anywhere that it bounces it would probably go out of bounds anywhere and then it goes right on his foot."
The Union (2-7-2) were still in the game at that point because of Konopka's solid work and wasteful finishing by Toronto. It was Konopka's first start of the season and only second MLS appearance.
"I'm extremely disappointed with that performance," said Union team manager Peter Nowak. "I mean we have a couple good games - we play the way we wanted to and today was completely the opposite.
"So we make two steps forward and three steps back."
Now winless in five games, the Union must refocus for a U.S. Open Cup game Tuesday against the Rochester Rhinos.
Toronto had the better of the chances but Konopka frustrated the home side time and again. It's because of him the Union weren't trailing by a few goals at the end of the first half.
Konopka did well in the ninth minute as a quick Toronto free kick near the halfway line resulted in Reggie Lambe bearing down on goal from the right side. Quick off his line, Konopka closed down the initial shot and while Lambe did get a second chance, he was forced out to a bad angle and was only able to put a ball across the goalmouth.
With five minutes left in the first half, Konopka had to be quick again as former German International Torsten Frings had a chance. But the Union goalkeeper got out so quickly that he prevented a shot and left Frings with no option but to lay the ball back, which the Union later cleared.
The Union's best chance to score came in the 50th minute as Michael Farfan let a rocket of a shot go from 25 yards away. The shot had TFC goalkeeper Milos Kocic beaten but not the crossbar as it rattled off the frame of the goal.