Jon Parkin's sixth goal in eight games condemned the Sky Blues to a third league defeat in a row.
The Sky Blues had led through Clinton Morrison's 18th minute strike, but a Ben Turner own goal and Parkin's 72nd minute finish gave Preston the points.
The Sky Blues started well on the bobbly Deepdale pitch, and put together some good passing moves in the opening stages.
However, it was Preston who forced the first real attempt. Chris Sedgwick crossed from the right only for Parkin to mis-kick the ball - but it fell to Stephen Elliott who curled the ball wide from 10-yards out.
Sedgwick followed up the move minutes later with an excellent deep cross to Parkin - but his outstretched boot could only turn the ball onto the roof of the net.
The close-call sparked City into life and an excellent move resulted in the opener.
Guillaume Beuzelin started the move in the centre of midfield, playing the ball to Stephen Wright. He played an excellent one-two with Jordan Henderson and burst into the Preston box before firing a low shot towards the corner of the net, which Morrison got a faint touch to score his first goal of 2009.
Preston responded well to the goal but missed three good opportunities to level in quick succession.
First, Parkin received the ball in the area but delayed his shot - which was eventually blocked by Scott Dann.
Two minutes later, Ross Wallace's cross found Elliott unmarked in the six yard box, but his rash volley went high over the bar.
Wallace then supplied another penetrating ball - a low cross - to find Parkin in a similar position, but the forward mis-kicked the ball and it was collected by Keiren Westwood.
Morrison had a bad miss of his own in the 25th minute - Henderson's through-ball put him clear but he could not connect cleanly with a shot and Andy Lonergan saved.
Morrison turned provider three minutes later and fed Henderson through - he fell under challenge from Sean St Ledger, but referee Keith Friend booked the winger for diving.
The game turned a little scrappy and after giving away a free-kick 30 yards from goal in the 37th minute, Preston had a fortunate equaliser.
Ross Wallace's put the ball towards the back post and Ben Turner, under pressure from St Ledger, headed the ball into his own net.
The Sky Blues came close to going back ahead with the final kick of the half, when Eastwood turned his marker on the edge of the box and fired a shot towards goal - only for it to rebound off the post and wide.
The second-half began slowly but Turner nearly had his revenge in the 54th minute. David Bell's corner bounced through the area and into the defender's path - but his shot was blocked for another corner.
Parkin came close again on the hour mark when the ball bounced to him in the area - but he failed to lift the ball over Westwood and his effort landed over the bar.
City were struggling to create chances, and were forced to shoot from range - a 35-yard half volley from Henderson the closest chance.
However, Parkin would give Preston the lead in the 72nd minute. Westwood took a City free-kick near the corner flag but it fell short to Paul McKenna. The captain knocked a ball over the top for Parkin to run onto, and after rounding Westwood, he finished coolly.
Robbie Simpson and Aron Gunnarsson were introduced to try and force a late equaliser but despite some good forward movement, Preston held out for the win.
Coventry City: Westwood; Wright, Turner, Dann, Hall; Henderson, Doyle (Gunnarsson 83), Beuzelin, Bell; Eastwood (Simpson 80), Morrison.
Subs: Marshall (GK), Ward, Osbourne.
Booked: Henderson 28, Beuzelin 31
Preston North End: Lonergan; Jones, Mawene, St Ledger, Nolan; Sedgwick (Whaley 71), Nicholson (Carter 59), McKenna, Wallace; Parkin, Elliott (Mellor 64).
Subs: Brown, Neal.
Booked: Parkin 68
Referee: Kevin Friend (Leicestershire)
