Doyle fired a 30-yard belter into the top-corner of goalkeeper Andy Lonergan's goal in the 85th minute, just five minutes after Dele Adebola had pulled the Sky Blues level.
The Lilywhites had gone into the game second from bottom and searching for a first league goal of the season.
Paul Simpson kept faith in Patrick Agyemang and the former Gillingham man put his side in front after 16th minute. Elliott Ward's back-pass to Coventry goalkeeper Dimi Konstantopoulos was cleared sluggishly and fell to Preston captain Kevin Nicholls.
His through-ball fed in Agyemang, who shrugged off Marcus Hall to coolly slot home from 16 yards.
But Coventry were not ready to give up their unbeaten run without a fight and could have drawn level after 29 minutes.
Leon McKenzie turned in the box and fed in Jay Tabb who scuffed his shot from eight yards. The ball was cleared, but only to Julian Gray who powered a looping header towards goal. The Sky Blues fans jumped to their feet, only for Darren Carter to clear the ball off the line.
Coventry continued their fight in the second half, while the Lilywhites sat back and sat on their lead.
City had chances early on with Hall heading a Michael Doyle free-kick onto the bar and McKenzie being denied by Lonergan after the goalkeeper flapped at a high-ball.
The Sky Blues came close once more when substitutes Ellery Cairo and Michael Mifsud linked up after 77 minutes. Cairo's deft cross found Mifsud six yards out, but the Malta international could only head wide.
But the breakthrough came minutes later when Ward's free-kick fell to Adebola in a crowded area. The Nigerian shrugged off his marker and turned smartly to fire a low-shot past Lonergan.
Preston were stunned and before they had chance to catch their breath, the ball fell to Doyle on the left. The Irishman fired in the effort into the goal to win the game and secure the three points.