Matt Tubbs, who netted his 23rd goal of the campaign, and Brad Halliday shared goals in the last seven minutes as Pompey ended their worst ever Football League season.
Waddock started five homegrown players – Jed Wallace, Adam Webster, Ben Close, Dan Butler and Conor Chaplin – before bring a sixth, Bradley Tarbuck on as a second half sub.
Waddock said: “You look at their age and you think I’m not sure, but you take their ages out of it you think that they are a good player.
“If they are good enough I am all for playing them. Injuries have opened the door for them to get first-team opportunities and they have taken their chances.
“I think there are positives to take but there are frustrations at the same time.
“Second half we played very well, created lots of opportunities but came up against a keeper in really good form.
“We have draw a line after this season and look towards the future, and hopefully it will be a bright future.”
Wallace, who looks set to have played his last game for Portsmouth with Championship clubs reportedly interested, crashed a back-post volley onto the inside of a post as the hosts turned on the pressure in the second half.
Before Tubbs was a whisker away from taking a deserved lead when his drive hit the frame of the goal.
Keith Lowe also hit the bar for York from an overhead kick early on, but neither side could end disappointing seasons on a high.
York manager Russ Wilcox piled the praise onto his young loan star from Middlesbrough Halliday.
He said: “It was a really good goal and it is great Brad got it, he has been outstanding for us .
“People forget he is only 19 and he has played in three different positions for us.
“To be honest he probably had his worst first half but in the second half I was delighted with him.
“It is a good way to finish the season it is great to get a point at a place like this.
“Bobby had to make two or three fantastic saves and it was a really exciting game.
“We will have a look at every position before next season and see what is required.
“We have a pretty strong spine to the team but we could improve the wide areas and the top end of the pitch because we haven’t scored enough goals
“It would be great to have a player like Matt Tubbs to win the tight games.”