Aside from defender Rui Marques, Leeds had a youthful side on show as the Whites got their second win on the trot in the Pontin's Holidays League after initial fears that, after heavy thunderstorms hitting York, that the match might have been called off.
City are managed by City captain and former Leeds defender David Wetherall.
In the early stages of the game itself the Whites had a penalty appeal waved away after a challenge from John Swift had upended Howson, then after a poor clearance from keeper Jonathan Lund, Brown was gifted an open goal, but he shot wide from 25-yards.
Brown was then booked for blocking a free-kick and on 30 minutes a crossfield pass from Patrick McGuire to Nick Smith gave City a goal opportunity. Smith passed the ball to Tom Penford but the Bantams midfielder struck the ball wide.
With 36 minutes gone City had the ball in the back of the net when a cross from Colbeck found Brown who chested the ball home, only for the goal to be ruled offside.
Leeds then broke into the area and a blistering shot from Howson was parried away by Ben Saynor.
The heavy rain returned in the second half and on 60 minutes, a good run from Danny Rose left Swift and Hopkins standing but as he ran into the area, his shot was saved by Saynor.
A long pass from City's Simon Ainge upfield to Smith enabled him to shoot on goal but Lund saved well.
Leeds eventually took the lead in the 66th minute when City conceded a free kick on the edge of the box and Swift became the second player to be booked, this time for dissent.
The wall was moved back ten yards and the free-kick was hit into the top corner by Howson after taking a deflection.
City nearly equalised straight away but Mitchell's effort was just wide. The bad weather returned and conditions became treacherous.
Just minutes remained when an error by Steven Mitchell gave Leeds' David Brown a great opportunity to double their lead, but his shot went well wide. Then a shot from Bayly hit the bar after a save from Saynor. Ian Morris also had a shot blocked and another effort saved by the City keeper.
United: Lund, Madden, Camfield, Wilkinson, Marquez, Hird, Gardner (D.Brown), Bayly, Morris, Howson, Rose (Hutton).
Subs Unused: Stansfield, Wilberforce, Ameobi.
City: Saynor, Swift, O'Brien, Mitchell, Ainge (Morgan), Clarke (Hopkins), Colbeck, McGuire, J Brown (Osbourne), Penford, Smith.
Subs Unused: Convey, Harper.