The Shrimpers, who only had two subs to call upon, came from behind to win 2-1 at Roots Hall on Saturday.
Will Grigg put the Spireites ahead in the first-half but a penalty from Jack Bridge and a deflected strike from Wesley Fonguck secured the three points for the hosts.
“To beat the calibre of team we’ve beaten makes it one of the best games I can remember here,” Maher told the Southend Echo. “It’s incredible. It’s right up there with the results we’ve had. Only having two subs and dealing with everything we have to is well documented.”
He continued: “All credit to the players. Off a defeat last week coming into playing the league leaders at home and with them taking the lead as well for the team to turn it round and to win the game is incredible. The performance from everyone meant it was fully deserved too.”
On the performance, said: “I knew we would play with energy and intensity but Chesterfield are a top team.
“We had two subs today and you knew when it got to 60 minutes and they’re bringing subs on that’s going to be a problem. But the players stood up to it and played really well. We kept plugging away and kept on pushing. When we got the first goal it was important to push on and try to win the game. We didn’t want to sit back.
“You can feel the positivity coming back and to have over 8,000 here was great. They stayed with the players even when we went behind. We’re grateful for that and it can help massively."