January signing Darren Murray scored the decisive goal in this contest at Solitude, with ex-Mallard Chris Curran adding a break away second on 94.
Murray has recently transferred from Portadown and was due to serve a one match suspension, but with the Ports playing on Tuesday evening his suspension was cleared, despite him no longer being with the club.
Ballinamallard started the game reasonably well with Jay McCartney going closest when his chip over Conor Devlin went narrowly past the post.
Cliftonville seen two efforts cleared off the line in the first half, both my Emmet Friars whilst Rouse also denied Murray.
Murray squandered yet another chance after the break but he made no mistake on 62 minutes. Martin Donnelly played a smart and quick free kick which slid Murray and he found the opposite corner of the net.
Substitute Ryan Mayse went close for the Mallards but his volley whistled past the left upright whilst there were also calls for a handball waved away by referee Raymond Hetherington, when Ryan Catney appeared to handle in the box.
With time running out the Mallards surged forward and were caught on the break on 94 minutes with Curran duly finished.
At Fisher Park, the seconds went down 3-2 to Cliftonville Olympic. The away side raced into a 3 goal lead but Johnny McKeown and Andy Little replied in the second half.
The thirds returned to action in the youth league cup and progress to round 2 after a solid 4-0 win over Knockbreda Youth. Jordan Breen got the opener, Jordan Cadden added two and Jacob Britton added another.