Hartlepool United came from two goals down to rescue a point at home to 10-man Newport County on Saturday afternoon.
Ten-man Shrewsbury scored a last-minute penalty to snatch all three points away from Dagenham & Redbridge.
Luton Town dropped off the top of the table as they conceded their 1-0 lead to Exeter City and were forced to settle for a draw. Wycombe Wanderers leapfrog Luton into first after coming from behind to beat Oxford United 2-1.
Northampton Town secured a 2-0 home win over AFC Wimbledon with a second with the last kick of the game, while Tranmere Rovers also scored at the death to rescue a point in their 2-2 draw with Stevenage.
Results in full: Burton Albion 1-1 Plymouth Argyle, Bury 2-0 Cambridge United, Cheltenham Town 0-1 York City, Dagenham & Redbridge 1-2 Shrewsbury Town, Exeter City 1-1 Luton Town, Hartlepool United 2-2 Newport County, Mansfield Town 1-2 Southend United, Northampton Town 2-0 AFC Wimbledon, Oxford United 1-2 Wycombe Wanderers, Portsmouth 3-0 Carlisle United, Tranmere Rovers 2-2 Stevenage.