David Meyler's first-half strike looked set to give Hull City an unlikely win at the champions and, while substitute Milner's free-kick denied the visitors, it does little to help his side's title defence.
Republic of Ireland international Meyler made the most of slack defending to grab the opener after 35 minutes before Hull were required to withstand plenty of pressure after the break.
Sergio Aguero rattled the crossbar late on as Steve Bruce's side seemed to have held on to frustrate their opponents and record what would have been their first clean sheet in five attempts, but Milner stepped off the bench to curl home the equaliser.
However, a below-par home side - who will be desperate for influential Ivorian midfielder Yaya Toure to return from Africa Cup of Nations duty - still slip seven points off leaders Chelsea after Jose Mourinho's side beat Aston Villa 2-1.
Though denied a fifth win of the Premier League season, Hull still clamber out of the bottom three on goal difference above Burnley.
Striker Edin Dzeko was one of three Manuel Pellegrini changes and he threatened down the left early on before Sone Aluko - brought in by Bruce as Hull's lone forward - tested Joe Hart soon after.
Despite their dismal run of form, Bruce's men acquitted themselves well and had the game's first clear-cut chance when Ahmed Elmohamady crashed a header against Hart's crossbar 15 minutes in from a deep Robbie Brady cross.
While the champions gathered themselves after that scare, Pellegrini's side continued to falter going forward and were eventually punished for their sluggish start when Meyler rewarded Hull's persistence.
Brady's effort was saved by Hart following a poor Martin Demichelis clearance before Gaston Ramirez hit the post as Fernandinho failed to deal with the danger.
However, when the rebound fell to Meyler, the midfielder made no mistake to open the scoring amid sloppy defending from Pellegrini's back line.
Pellegrini responded at the break by taking Fernando off for Jesus Navas and his side responded well as Dzeko connected acrobatically with Pablo Zabaleta's cross to threaten Allan McGregor's goal.
David Silva then saw penalty appeals waved away by Jon Moss as he went down under clumsy contact from Alex Bruce as the home side continued to knock at the door.
The otherwise quiet Aguero almost gained his side a point late on as he controlled the ball with his right foot before unleashing a stunning strike against the crossbar with his left in the final minute of normal time.
Pellegrini's men were eventually rewarded for their second-half onslaught thanks to Milner's perfectly despatched free-kick, although the Chilean has plenty to ponder in his quest to reel Chelsea in at the summit.
