Danny Rowe bagged a hat-trick and Saidou Khan notched the other.
The match was interrupted in the second-half when protesting Southend fans invaded the pitch to voice their anger at chairman Ron Martin.
The victory was Town’s first in four and it moves them up a place to fourth in the National League table.
Here are Liam Norcliffe’s player ratings from the game...
9. Saidou Khan 7
Got his third goal in a Chesterfield shirt and the Spireites' third on the day as he finished at the far post just after half-time. Had to come off injured with 25 minutes to go. Photo: Tina Jenner
10. Danny Rowe 9
Scored a hat-trick including two classy finishes and a thumping penalty. He was superb in general and one mazy run deserved another goal. He was also involved in Khan's goal. Photo: Tina Jenner
11. Kabongo Tshimanga 7
Came close to scoring in the first-half but he hit the side-netting. He won the penalty when he was bundled over in the box. Photo: Tina Jenner
12. Jamie Grimes 7
He came on for the injured Kerr after half an hour and slotted into the right centre-back spot with ease. Photo: Tina Jenner