Both Phillips, who had been on the pitch for only five minutes, and team-mate Lee Canoville initially claimed the goal. But Phillips later confirmed that he had forced Canoville's goal-bound header over the line.
The former Manchester City and Plymouth winger had come off the bench to score another late goal the previous weekend, but that effort was only a consolation goal in a 4-1 defeat at Barnsley.
This time it could have a major bearing on Torquay's hopes of staying up, even though results elsewhere dropped them into the bottom four.
Torquay took a 20th minute lead when leading scorer Adebayo Akinfenwa volleyed in his 11th goal of the season from a diagonal cross by Tony Bedeau.
Alex Russell also hit the bar, before Chesterfield, managed by former Torquay boss Roy McFarland, hit back to equalise and then take the lead early in the second half.
Derek Niven struck a fierce 25-yarder past Torquay's debutant keeper Andy Marriott in the 31st minute.
And Mark Hudson robbed Bedeau on the edge of his own area before chipping Marriott from 22 yards in the 50th minute.
Chesterfield looked increasingly secure as the second half went on, forcing Marriott into one good save from Jamie McMaster.
Torquay were running out of ideas before Phillips went on in the 84th minute.
He forced a brilliant tip-over save from Chesterfield keeper Carl Muggleton in the 88th minute, but the corner saw Russell deliver the ball to the near post and Canoville's header was on its way into the net before Phillips made absolutely certain.
MK Dons' home win over Stockport dropped Torquay into the bottom four and they have a daunting series of games coming up. They meet promotion-chasing Hull, Sheffield Wednesday, Bristol City and leaders Luton in four of their next five games.
Head coach Leroy Rosenior is grappling with an injury crisis in defence which forced him to play with several men out of position.
They are expected to strengthen their squad still further next week after handing debuts to veteran keeper Marriott and former Cambridge and Norwich striker Zema Abbey against the Spireites.