David Hopkin named a youthful starting line-up which included three trialists and just one player with first-team experience in Declan McDaid.
Ton went in at the break on level terms after trialist Michael Thomson scored with a 20-yard strike which looped over Ayr goalkeeper William Muir.
However, half-time substitute William Boyd was shown a red card just one minute into the second period for a straight-legged tackle.
This left an inexperienced side - of the 16-man squad, six were under-17 players from the club's youth academy - facing an uphill struggle in the remaining 44 minutes.
They struggled to cope and eventually conceded four more as the Honest Men eased to a convincing Cappielow win.
With four of their seven Reserve League Cup fixtures completed, Ton remain second bottom of the west section, level on points with Ayr who prop up the table.
Hopkin's side are back in action on Thursday 25 April when they face Rangers' second string at Murray Park. Kick-off is 7.30pm.
Morton (4-4-2): Murray [Trialist]; Keogh (Boyd, 46), Verlaque, Jamieson, Knight; McLaughlin, McLean, Nicolson (Lamont, 47), McDaid (Cairnie, 46); McNeil [Trialist],Thomson [Trialist]. Subs not used: O'Neil, Russell.