Stevie May opened the scoring for the home side before Nigel Hasselbaink secured the points at McDiarmid Park.
The win allowed Saints to move into the top half of the table, while Motherwell squandered the chance to claim second spot.
McCall said: "I'm naturally disappointed. It was an uncharacteristic performance from us. We were off it and we got beat. I didn't see it coming.
"The conditions don't make it great for great football but, when the conditions are like that, you have to look to win it in different ways.
"But St Johnstone deserved their victory."
The second goal was gifted to Saints after goalkeeper Gunnar Nielsen slipped on the wet surface but McCall refused to point the finger of blame.
He said: "He came in and held his hands up but anyone can slip. It was just unfortunate.
"The second goal killed us but I still don't think we did enough in the game to merit anything."