Stewart feels the progress the former St Johnstone boss has made at the Reebok Stadium shouldn't just be forgotten after their 5-0 FA Cup semi-final mauling at the hands of Stoke City.
He told the Daily Record: "It's up there with the worst disappointments in my life. To go to Wembley and lose 5-0 has left us as low as we could get.
"What hurts is we knew we had a fantastic chance to go back for the final so we have to try and lift each other after this. It's my job to make sure Owen's okay, which I'm sure he will be as he's a strong character.
"We've got a big game coming up against Arsenal so we have to be ready for that. We've had a good season, let's not forget that. It's a setback in the sense of what we've achieved this season.
"But I wouldn't like to think people will judge Owen on this one result. We've all had bad days. Look at the history books and you'll see even Sir Alex Ferguson has had a few along the way.
"The job that Owen's done this season shouldn't be tarnished by Sunday. Remember, we had to beat Birmingham and Fulham away to get to Wembley.
"It's disappointing to lose like that on the big stage, of course, but no way will we let it get us down."