The former Kilmarnock manager watched this game from the stand as caretaker David Hopkin took charge for the last time, but he will now put his own hallmark on a team now five points adrift at the bottom.
In truth, Morton matched Alloa for long spells, particularly with the wind at their backs in the second half, but there was always more menace about the home side.
They took the lead three minutes from the break when what looked like an over-ambitious shot from distance from Kevin Cawley troubled goalkeeper Nicolas Caraux.
Caraux could only divert the ball into the path of Andy Kirk and the Irishman struck the opener, his sixth goal of the season.
Morton's Scott Taggart saw a long-range shot touched past the post by the alert Scott Bain in the second half, but Alloa were organised at the back and dangerous on the counter-attack.
Cawley and substitute Eddie Fearns failed to take goal chances, but the points were assured with five minutes left when Fearns squared to on-loan Declan McManus and he touched home the second goal just three minutes after coming on.
Dundee suffered a 2-1 defeat by Cowdenbeath at Dens Park as Hamilton took over at the top of the table. Cowdenbeath should have taken the lead when Gary Irvine handled a Kane Hemmings' shot in the penalty area, but Jon Robertson's spot-kick was brilliantly saved by Kyle Letheren. Dundee did not heed the warning and Robertson struck the crossbar with a header at the start of the second half.
It was no surprise when Hemmings put Cowdenbeath in front when he guided home a shot early in the half.
Dundee equalised in 65 minutes, Jim McAlister scoring with a low shot at the edge of the area after running at the Cowdenbeath defence.
But Jordan Morton struck what proved to be the winning goal five minutes later.
Livingston and Hamilton fought out a drab 0-0 draw at Almondvale as the weather crippled both teams.
Burton O'Brien came closest to breaking the deadlock after the introduction of Mark Burchill and Martin Scott prompted the midfielder to try his luck from just outside the box, rattling the woodwork with a powerful drive.
Raith Rovers beat Dumbarton 2-1 in spite of having to play the final half hour without Joe Cardle, who had been sent off for a wild challenge on Mark Gilhaney.
Grant Anderson struck the crossbar for Raith and the home side edged in front six minutes after the break when Lewis Vaughan connected with Calum Booth's low cross.
Jason Thomson fired home a second goal in the 74th minute from Vaughan's pass before substitute Steven McDougall pulled one back in the final minute.
Queen of the South's game with Falkirk was abandoned by referee Iain Brines after 27 minutes due to high winds with the score at 0-0.