Maguire swivelled and smashed home a knock-down from a corner in the 85th minute to maintain England's perfect start to their Group I campaign.
England had dominated the majority of the match at Wembley, taking the lead after 19 minutes when Harry Kane fired home from the penalty spot. Things turned sour for Gareth Southgate's side, however, when Stones allowed Jakub Moder to level in the second half.
Stones dawdled on the ball and Poland midfielder Moder robbed him of possession before firing home after a quick exchange of passes.
The win lifted England to nine points from three games, two ahead of Hungary in second with Poland on four points.
Poland, shorn of their main attacking threat with Bayern Munich's striker Robert Lewandowski ruled out by a knee injury, were never likely to tear into England and their more defensive approach frustrated the hosts in the early stages.
England lacked any sort of penetration or attacking impetus in a stale opening, but suddenly found an extra gear with Sterling's pace causing trouble for Poland's three-man backline and drawing the penalty that delivered the opener.
Kane stepped up to wallop the ball down the middle and become England's all-time leading penalty scorer with 10 goals from the spot.
The Poles did well to reach halftime without conceding again, Sterling twice failing to get a shot away when chances opened up in front of him and Kane stinging the palms of Poland keeper Wojciech Szczesny with a rasping effort.
England were in total control but handed Poland a route back into the match when Stones dwelt on the ball and allowed Moder to steal in.
The goal seemed to draw the sting from England's attack and the hosts laboured for the rest of the game.
Maguire, however, rode to their rescue when he latched onto Stones's knockdown and thumped home from eight metres.