Relieved Michael O'Neill felt his Stoke side were full value for their first Championship win in 10 attempts.
It was their first success since December 19 and gave their promotion hopes a shot in the arm.
He said: "I'm relieved and pleased for the lads because they have given a lot. In recent weeks there have been games where we have deserved more.
"I thought we were always in control without being as effective as we could have been.
"In the second half we create chances but didn't look like we'd take one, but then Fletch did take one and we thoroughly deserved it. Hopefully now we can string some results together."
On his matchwinner, O'Neill added: "He looks back to the player he was before he got injured.
"We brought him to the club for his all-round play and his link-up is good, but I'm pleased for him to score against his old club, that's always a good thing."
The sides had shared a goalless draw at Hillsborough in November and this encounter looked to be heading the same way as a lack of quality told in front of goal.
After an even first half, Stoke dominated the second but wasted their opportunities.
Allen should have broken the deadlock on the hour but sidefooted the ball wide and time began to run out.
But the clincher came when Fletcher swivelled in the box to prod home from close range.
Wednesday caretaker manager Neil Thompson said: "I'm very disappointed.
"First half was very nip and tuck and we were very disciplined. I knew it would be a physical type of game but we didn't have too many problems.
"But in the second half we never got started. We sat back further and further and it was a sucker punch at the end.
"You can't give Stoke's quality players that encouragement. I thought we'd weathered it and then you can't lose (Steven) Fletcher in the box.
"We have to dust ourselves down and get on with it.
"We have been inconsistent for a lot of the season and those performances keep creeping in. We didn't ask enough questions of them and we have to bounce back quickly."