Although pleased with the overall outcome, the assistant manager was disappointed with the first half when his side could easily have found themselves behind despite 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.
Nicholl said: "We had a great start to the game and although we were lucky to get the own goal I thought 'here we go'.
"Then we did nothing except face waves of attacks from Motherwell when we just couldn't get the ball out of our own half.
"I said to the players at half-time that they didn't have a chance of winning the game if they continued like that - and I'm sure they were sitting in the Motherwell dressing room wondering how they weren't ahead."
Well boss Stuart McCall was unsurprisingly frustrated and lamented missed chances in the first half.
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."