Former Barnet manager Martin Allen saw his MK Dons team grab a late equaliser to earn him a point on his first return to Underhill since leaving in 2004.
Ian Hendon had put Barnet ahead with a penalty but Sean O'Hanlon equalised from Dean Lewington's corner.
Tresor Kandol restored Barnet's lead after a flowing move and then crossed for Richard Graham to make it 3-1.
Ben Chorley pulled one back with a penalty before Lloyd Dyer fired home from Chorley's long pass to level.
Barnet: Harrison, Hendon, Gross, Charles, King, Hessenthaler, Graham (Cogan 81), Bailey, Sinclair, Kandol (Vieira 90), Hatch.
Subs Not Used: Flitney, Nicolau, Grazioli.
Booked: Bailey, Hendon, Hessenthaler.
Goals: Hendon 38 pen, Kandol 52, Graham 57.
Milton Keynes Dons: Baines, O'Hanlon (Jamie Smith 76), Lewington, Diallo, Chorley, McGovern, Mitchell (Edds 83), Wilbraham, Dyer, Platt, McLeod (Taylor 66).
Subs Not Used: Bankole, Crooks.
Booked: Chorley, Diallo.
Goals: O'Hanlon 43, Chorley 69 pen, Dyer 90.
Att: 2,819
Ref: T Kettle (Berkshire).