However, despite the loss the Kiwi revealed he saw enough positives during the match to give him hope that things will soon be heading in the right direction.
“I feel really bad for the guys,” he said after the game.
“They worked their socks off and put a real shift in. They had a really good first half in which I really feel they dictated the game and had a couple of very good opportunities. If we had taken one of those, it would have been a whole different ball game.
“We’ve played away from home and delivered a very good account of ourselves and had some very good chances. This team will only get better.”
In an eventful week leading up to the season opener Toronto lost captain Torsten Frings, who announced his retirement from the game, and a number of new players including Welsh international Robert Earnshaw signed with the club.
Nelsen said, despite the result, it was an encouraging performance under difficult circumstances.
“We had three or four guys out there who are just back from injury or who were new to the team,” Nelsen said.
“We knew Vancouver would come back at some stage and come hard at us. There were 15 minutes in the second half that we just had to get through and unfortunately what was a pretty routine long ball ended up being a case of us not winning the second ball and it resulted in a goal.
“Vancouver were really kind of dictated to in the first half, and I thought we played extremely well,” Nelsen said. “I thought we showed our strength and character, and we were always in the game.”
The next match for Toronto FC is their home opener against Sporting Kansas City at the Rogers Centre on 9 March.