Lee, who has not played a competitive match for over 15 months, helped Neil Thompson's side end their season on a high note.
It was Lee's second run-out for the Under-23s in the space of a week. He also featured in the first half of the home win over Watford.
The 30-year-old, out of contract at the end of the season, resumed full training a number of weeks ago.
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But manager Steve Bruce quickly dismissed the possibility of Lee or Matt Penney, who underwent shoulder surgery in January, figuring before the end of the regular season.
Speaking after their goalless draw with Stoke City at the end of March, Bruce told The Star: "I can't see Kieran Lee or Matt Penney being available for us this season.
"I think I have got to dismiss that as there are only five weeks left."
A double from Bulgarian striker Preslav Borukov helped Wednesday defeat QPR. Borukov also struck the post with a left foot drive in the second half.
Ash Baker, Jack Lee, Connor Kirby, Fraser Preston, Alex Hunt and Penney, making his long-awaited return to action following a lengthy injury lay-off, all featured in a strong Owls side.
Victory sees Wednesday finish in eighth position in the Professional Development League Two North table. The result lifted them above neighbours Sheffield United, who were held to a goalless draw at Millwall.