Nicholl, who is deputising for boss Kenny Shiels while he serves a four-game touchline ban, felt Kilmarnock were poor in the first half and could easily have found themselves behind before an own goal from Stevie Hammell and William Gros' strike gave them the points.
Their task was made easier in the closing stages when Motherwell were reduced to nine men after Fraser Kerr and then captain Keith Lasley were shown straight red cards for wild tackles on James Dayton.
"We had a great start to the game and although we were lucky to get the own goal I thought 'here we go'," said Nicholl.
"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.
"We took off (Borja) Perez to try and get a grip of the game and I think we need to praise the players for defending and taking their chances and having the game won before they had two players sent off."