Goals from Liam Craig and Nigel Hasselbaink sealed the win but Well were already confirmed as runners-up in the SPL.
McCall said: "I was disappointed we lost the game.
"There are no excuses. St Johnstone had the bit between the teeth. I don't like losing anything but we have to take a reality check.
"It's not been about that, it's been about the season."
McCall has been linked with Doncaster and Sheffield United but said he was planning for the future at Fir Park.
He added: "It's all speculation and until someone asks to speak to me, that's what it is.
"We are certainly planning. We gave Simon Ramsden a two-year deal a couple of days ago.
"We will hopefully tie up a deal on Monday for a new player coming in.
"You've got to be planning."