Goalkeeper Connor Ripley was the only member of Jamie Clapham's squad with first team experience, while City included former Boro loanee Alex Nimley up front.
Patrick Vieira and ex-Boro forward Brian Marwood, both now senior members of City's executive, both attended as part of a large staff contingent.
Nimley had the game's first chance when his 25-yard effort was deflected over the bar for a corner, which was cleared.
Ryan Brobbel was next to come close as his dipping, long-range shot landed on the roof of the net on 18 minutes.
However, Boro didn't have long to wait for a breakthrough.
The impressive Lewis Sirrell scored with a controlled finish after Boro put City on ropes with a good spell of pressure involving Matty Waters and Wilson Kneeshaw.
Carlos Tevez lookalike Marcos Lopez blazed into space before firing across the face of goal as City tried to regain the upper hand.
But Boro grew in strength and could have gone further ahead when skipper Matthew Dolan just failed to make contact with an attempted volley.
But City gave a reminder of the threat they posed asOliver Ntchum struck the outside of the post following a clever free-kick routine.
And captain Kareem Rekik levelled for the visitors soon afterwards on 40 minutes, firing in a close range shot across the diving Ripley.
Nimley made way for Devante Cole, son of former England striker Andrew, shortly before the break.
Soon after the restart City took the lead as Marcos Lopez poked the ball home following a goalmouth scramble.
The game continued to ebb and flow and there were plenty of strong but fair challenges from both sides in what was a competitive encounter.
But Boro got stronger as the half went on and it was no surprise when the equaliser came, on 74 minutes.
Ryan Brobbel scored it with a cracking shot after Kneeshaw's effort was well saved and a follow up hit the post. The goal followed a typical surging run from left-back Paul Weldon.
Kneeshaw almost won it for Boro at the death but saw his fierce shot blocked, then City came close through Hutton with seconds remaining.
However, it was honours even at the final whistle as Boro prevented City from recording a double following their 4-0 win earlier in the campaign.
Boro: Ripley, Bennett, Weldon, Dolan (c), Burgess, Oliver, Fowler (Jones 57), Brobbel, Waters (Fewster 71), Kneeshaw, Sirrell (Edwards 66). Unused subs: Rivers, Montgomery (gk).
City: Johansen, Leigh, Meppin Walters, Glendon, Kennedy, Rekik (c) (