Nugent was an injury concern leading up to the game after he was forced off with a neck problem in the 2-2 home draw with Nottingham Forest the previous weekend.
But the striker started against Ipswich and scored twice to quickly put the Foxes 2-0 up and take his tally to nine goals for the season.
However, Nugent was denied the chance of a hat-trick as he was replaced by the fit-again Jamie Vardy after only half an hour of the 6-0 victory.
Shakespeare said: "It's nothing to worry about. We took him off more as a precaution. He hadn't trained fully all week and declared himself fit, but we didn't want him to make his neck injury any worse.
"When you are in a nice position of being able to bring Jamie Vardy on, it was about giving him the rest."