The Martyrs are unbeaten after three successive games against the basement clubs.
But they won this lack-lustre match with a penalty in stoppage time (writes Phil Howells)..
Owain Jones, a former Swansea City player, marked his debut with a spectacular goal for Merthyr, coming on for Corey Jenkins who took a knock and went off after 11 minutes.
Jones spent time on loan with Yeovil last year and has represented Wales at Under 16, 17, 19 and 21 level.
Merthyr forced two successive corners before Jones gave them the lead on 16 minutes, firing into the top far corner from outside the box.
But on 28 minutes Danny Watson levelled from a spot-kick after Scott Tancock had fouled Peter Clark. However, Tancock said afterwards it was rather "a soft penalty".It seemed that there had, however, been contact.
That setback saw Merthyr lose their grip with passes going astray. Tim Trebes in the St Ives goal,was kept busy at times but it wasn't easy for the home side with striker Ryan Prosser ill, meaning postponement of the presentation to him after his 300th appearance for the club.
The second half saw the Cambridgeshire visitors step things up and they led on 63 minutes, Ben Baker, unmarked,firing past 'keeper Oliver Davies.
Kerry Morgan, back after injury, replaced Harry Franklin on 58 minutes and with eight minutes left, it was Morgan who equalised. He chased through after the ball came across from another substitute, Lee Price, and drove home a fine goal.
It looked all set for a stalemate but Merthyr went on to get a somewhat fortunate win. Three minutes into added time and captain Charlie De'ath blatantly brought down Ian Traylor who got back up to fire home a dramatic winner. They moved up to 17th place in the table with 41 points from 35 games.
St Ives, who have earned more away points than at home this campaign, rued their several missed chances, as their directors agreed afterwards.