Tranmere substitute Mustafa Tiryaki scored the winner after just three minutes on the pitch against Walsall.
After a first half bereft of decent chances, the Merseysiders took the lead when Robbie Weir sent a rasping shot into the top corner from 25 yards.
Andy Butler's close-range header, from Jamie Paterson's cross, then levelled it for the Saddlers.
Tiryaki tapped in the winner before Walsall's Richard Taundry struck the bar with a 90th-minute free-kick.
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Tranmere manager Les Parry told BBC Radio Merseyside:
"It was a good performance from two very hard working sides.
"I was made up for Mustafa Tiryaki and I actually said to him you're due a goal, so I was made up he scored.
"Enoch Showunmi worked really hard and was looking a bit tired and sometimes a centre-half can get comfortable with a centre forward and that was the reason why we made the change."