Colchester United gave themselves a two-goal cushion after breakaway efforts in each half but Wilson came off the bench to net a fine solo effort with Baker firing home a superb free kick in added time.
City boss Steven Pressley made one forced change to his side for his home managerial debut, bringing in Cody McDonald for the injured Leon Clarke.
It was Franck Moussa though who registered the first effort of the evening on target after four minutes when he sprinted through the midfield before firing at goal, 'keeper Sam Walker saving with his legs.
City went close again from the resulting corner when Carl Baker's delivery was cleared only as far as William Edjenguele who headed the ball back into the danger zone for Aaron Martin to half volley inches wide.
Baker then did well after eight minutes, turning Bradley Garmston inside out to get to the byline and fire in a low cross which was untidily beaten away.
City fans were left with their heads in their hands though just moments later when McDonald did well to burst in between two defenders and tap a finish around Walker, only to see the ball hit the inside of the foot of the post and roll across the goal for Colchester to clear.
The game was ten minutes old when Colchester managed their first effort on target when Garmston intercepted a pass in midfield but could not get around Martin, his shot from the edge of the area forcing a comfortable save out of Joe Murphy.
McDonald kept the U's back four on their toes at the other end though when he out-fought Garmston and Magnus Okuonghae to a hooked ball from Baker although his finish hiot the side netting as he was pushed out wide on his way through the area.
The first 20 minutes really did belong to the Sky Blues as their flowing display had the visitors pegged back in thir own half.
Colchester almost undid their own defence after 18 minutes when a dangerous cross from Cyrus Christie saw Josh Thompson's headed clearance flash across his own goalmouth.
Walker was required again
two minutes later when a swift break from City saw a throw from Murphy release Moussa to bomb down the left flank, cut inside and the shoot with Walker parrying the shot away.
It was an almost identical attack from Colchester straight after when former Sky Blue Clinton Morrison sped down the left and cut a ball backl for Billy Clifford whose curling shot from 20 yards was pushed around the post by Murphy.
Colchester's opener six minutes before the break then came completely against the run of play.
Massey picked up the ball midway inside City's half and burst through the heart of the defence before poking a finish past Joe Murphy.
The disappointing end to the first half did not seem to deter the Sky Blues though as they came out for the second half clearly intent on passing the ball.
Their approach created an opportunity for James Bailey on 54 minutes when Dickinson cut inside from the left and laid a ball on for the midfielder who shot from 20 yards and forced a low save out of Walker.
City very nearly unlocked the Colchester defence again two minutes before the hour when Baker chased a long ball, turned his marker and then shot at goal, the effort taking a deflection into the path of Gary McSheffrey who tried to toe the ball home only to find Walker who came swiftly off his line.
Dickinson then found himself with a glaring opportunity four minutes later after a great bit of interplay with McSheffrey who he swapped quick passes with in the area before lashing a shot across goal and wide from ten yards.
It was the visitors who got the second goal though, again against the run of play, when a half cleared ball was headed back into the City area to the feet of Smith who poked a finish through the legs of Murphy.
City got the goal their play deserved though 14 minutes from time courtesy of a superb solo effort from sub Wilson.
The young striker picked up the ball midway inside Colchester's half and produced a series of step-overs to confuse his tracking defenders before firing inside the bottom corner.
Wilson then very nearly turned provider with eight minutes to go when his neat one-two with fellow sub John Fleck let in the Scotsman to fire at goal only to see his effort deflected just over the bar.
City got the grandstand finished they deserved as well as they still trailed heading into added time.
Bailey won a free kick on the edge of the area and Baker curled home a pinpoint effort past Walker and into the net and rescue a point.
Attendance: 9,431, (173 away)