Rotherham had dominated the opening 45 minutes, but found themselves on the back foot thanks to former player Kevin Ellison.
The midfielder netted the opener after benefiting from a great solo run and pass from Jack Redshaw after 29 minutes.
It was one of the few times the visitors crossed the half way line as Rotherham battled to find a way through Morecambe's defence. Shot after shot was blocked and Barry Roche was forced into saves by Kari Arnason and Lee Frecklington.
After the break, Morecambe pulled everyone back and challenged Rotherham to break them down. After 20 minutes of trying, that's just what they did.
After 64 minutes Arnason's cross took a wicked deflection wide of Roche and the lurking Nardiello turned the ball home from close range. Less than a minute later, Robert Harris picked out Nardiello with a pin point cross and he slammed the ball past a helpless Roche to secure victory for his team.