Notts County fans turned on manager Steve Thompson as Bury eased to their third away win in a week.
County started brightly and Adam Tann's header hit the bar but Bury seized control when Steve Haslam's speculative 30-yard shot put them ahead.
Neil MacKenzie levelled from the spot after Colin Woodthorpe handled.
But Paul Scott marched through to restore the lead and victory was completed when Tann felled Glynn Hurst and Nicky Adams netted the penalty.