The Azzurri had slim hopes of overhauling Spain to finish top of the pile, but two dropped points in their penultimate game - coupled with a convincing win for La Roja elsewhere tonight - put paid to that.
Despite dominating possession, Gian Piero Ventura's men were struggling to create too many openings and news soon filtered through of a 3-0 lead for Spain over Albania - essentially killing off their hopes of finishing top.
The Azzurri did at least have a lead to take into the break, though, thanks to Chiellini's tap-in after being picked out by an unselfish Ciro Immobile.
Seven of Italy's last nine goals in qualifying had arrived in the second half of games prior to this one, but a failure to convert possession into chances would come back to haunt them.
When Macedonia's equaliser did eventually arrive there could be few complaints following a spell of pressure, as the Red Lions stepped things up to breach the Italians' defence on home soil for the first time in four games.
Trajkovski was played in by Goran Pandev, who plies his club trade at Serie A club Genoa, before superbly finishing at the back post from a tight angle.
Italy's record of never losing a home World Cup qualifier, now standing at 54 matches, was never at risk in the remainder, as Macedonia put enough bodies behind the ball to ensure that there would be no time for a winner at either end.