The stalemate at Cappielow meant the Greenock side missed an opportunity to climb away from the foot of the cinch Championship table and MacPherson paid the price within a couple of hours of the full-time whistle.
"The club can today announce that, following today’s game, manager, Gus MacPherson, has been relieved of his duties," said a Morton statement.
"We would like to thank Gus for his efforts and hard work during his time at the club and wish him all the best for the future.
"The club will provide a further update in the coming days."
Morton opened the scoring after 26 minutes when Gozie Ugwu headed a Gavin Reilly delivery back across goal and into the far corner of the net.
They held on to that lead until the 73rd minute when Steven Bradley fired in off the crossbar, and then Tomi Adeloye put the visitors in front four minutes later.
Ugwu headed a second with six minutes remaining to ensure Morton did not come away empty-handed. But the result leaves them as part of a bottom three alongside Queen of the South and Dunfermline, all level on 13 points, and the club will hope a new manager sparks a change in fortunes.
Elsewhere, David Moyo scored a second-half penalty as Hamilton returned to winning ways with a narrow 1-0 victory over 10-man Dunfermline at New Douglas Park.
The hosts enjoyed the better of the early chances, with Josh Mullin and Marley Redfern both testing Pars goalkeeper Owain Fon Williams within the opening 12 minutes.
Teenage midfielder Redfern came close with a second shot on target midway through the first half but former Accies stopper Williams safely collected the ball, while - at the other end - Lewis McCann struck the crossbar as it remained goalless at the break.
The match came to life on the hour mark as Dunfermline midfielder Graham Dorrans was sent off for handball in the box, with Moyo firing the resulting spot-kick into the bottom corner for his second goal in two games.
The visitors looked for an equaliser and Josh Edwards came close before his header was blocked and Hamilton held on for full points for the first time since October.
Partick Thistle missed the chance to move a point behind leaders Inverness after being held to a goalless draw at Queen of the South. The Jags’ Lee Connelly hit the woodwork twice in the closing stages of the first half.
Raith Rovers had the chance to move top of the division but also had to settle for a 0-0 draw at Arbroath. The stalemate extended Rovers' unbeaten run to 12 league games, leaving them one point behind leaders Inverness.
Arbroath had a chance to open the scoring early on when Joel Nouble had a header blocked, and Rovers goalkeeper Jamie MacDonald did well to keep out Bobby Linn's effort in the 71st minute after the substitute broke from a corner.