The visitors found themselves behind due to Stevie Hammell's early own goal.
William Gros, who had earlier made three goal-line clearances, deservedly scored the clinching second goal before Motherwell's frustrations got the better of them in the closing minutes, with first Fraser Kerr and then captain Keith Lasley shown straight red cards for wild tackles on James Dayton.
Gros twice denied Shaun Hutchison and then hacked clear after Simon Ramsden's header was turned against the crossbar, while Lasley blazed over.
McCall said: "If it was a boxing match it would have stopped at half-time but credit Kilmarnock for the numerous blocks on the line.
"I thought we were rusty in the first 10 minutes but dominated the half-hour after they scored, but just couldn't put the ball in the net.
"We didn't play as well in the second half but they didn't create a lot of chances until we went down to nine men.
"I am not happy as we lost our discipline. Fraser Kerr has had a swipe at the ball and caught the player and Keith Lasley's challenge was born out of frustration, but it is not acceptable."