United held but remain top
At the other end of the table, Boston and Swansea remained in the bottom two as Carlisle beat the former 4-2 and Torquay came away from Wales with a single goal win.
Pawel Abbott had put Bury ahead in the 20th minute, with a well placed shot from around 15 yards out. However, with nine minutes remaining Richie Humphrey's cross found Adam Boyd unmarked in the six-yard box and he headed home.
Cambridge put an end to York's good run of form, a goal from Dave Kitson in the 13th minute set them on the way, yet the result was in doubt until eight minutes from time.
Then two goals in two minutes through Adam Tann (82) and Dave Bridges (84) completed the scoreline.
Brian Flynn's first game in charge of Swansea ended in defeat as David Graham's strike, thundering in a 25-yard drive in the 31st minute gave Torquay all three points.
Boston were stunned by a Brian Wake hat-trick at Carlisle and never really recovered from being three goals down.
Wake scored the first, beating the keeper to the ball in the 14th minute and it was two soon after when Richie Foran picked himself up to fire home a penalty.
In the 34th minute Wake made it three, heading home a cross and although James Cook pulled one back for the visitors Wake restored the three goal lead on the stroke of half-time and in the process completed his hat-trick.
Stuart Douglas managed a stunning volley in reply for Boston in the 69th minute but it was too little to make much impression on the game.
Lincoln continued their fine start to the season as they managed a 2-1 win over Southend Unied. Peter Gain gave the home side the lead with a stunning strike that saw him beat a couple of defenders before unleashing a crashing drive into the top corner.
Simon Yeo headed home a second in the 71st minute and although Neil Jenkins blasted in an impressive free-kick, the visitors could not get back on level terms.
Bristol Rovers were the top scorers of the day as they romped to victory at Shrewsbury Town.
Guiliano Grazioli (pictured) did most of the damage with a hat-trick - scoring in the 32nd, 52nd and 65th minute. Vitaly Astafjevs and Wayne Carlisle also scored for Rovers whilst Karl Murray (47) and Luke Rodgers (72) replied for The Shrews.
Two goals in the last 11 minutes was not enough to save Macclesfield from defeat at home to Scunthorpe. The Iron had romped into a three goal lead through a brace from Steve Torpey and a one from Martin Carruthers.
A Danny Whittaker penalty and Kyle Lightbourne got it back to 2-3 but The Silkmen could not find the equaliser from anywhere.
Alan Connell's 82nd minute equaliser saved a point for Bournemouth as they managed a 2-2 draw with Darlington. Derek Holmes put the South Coast men in front in the 27th minute but efforts from Graham Fenton and Barry Conlon had put the North-East side in front.
Paul Hall's second of the game in the 79th minute gave Rushden and Diamonds a share of the spoils at home to Wrexham.
Carlos Edwards got the opening goal in the eight minute but Hall's first (42) levelled matters. The Welshmen were back in front through Andy Morrell only for Hall to get his second and earn a point for his side.
Exeter pulled away from the bottom end of the table with a 1-0 victory over Leyton Orient. Matt Joseph was sent off for a professional foul in the box and Andy Walker struck home the resulting penalty.
Rochdale were held on their travels at Kidderminster in a scoreless draw and the result was mirrored at Oxford, where Hull City too left with a point.
Click below for more information on the relevant fixture:
Division Three
Bury v Hartlepool
Cambridge v York City
Carlisle v Boston
Darlington v Bournemouth
Exeter City v Leyton Orient
Kidderminster Harriers v Rochdale
Lincoln v Southend
Macclesfield Town v Scunthorpe
Oxford v Hull City
Rushden & Diamonds v wrexham
Shrewsbury v Bristol Rovers
Swansea City v Torquay United
Rushden & Diamonds v Kidderminster Harriers
Click here for the Division Three table