Cristian Montano was a constant threat, testing Magpies goalkeeper Scott Loach with an early shot, before bursting into the box to score before half-time.
Notts had gone close through Wes Atkinson and Izale McLeod, but Lee Brown got Rovers' second after the break when he fired in from 18 yards.
McLeod missed with a header as the hosts made a late fight-back.
The defeat comes days after chief executive Julian Winter left the club for Huddersfield, while angry home fans raised a banner in the Kop that was removed by stewards.
Bristol Rovers kept up their League Two promotion bid by consigning Notts County to a fifth game without victory.