Ash Taylor proved the match winner for Tranmere in his first appearance of the season.
The centre back netted the equaliser late in the game before scoring the winning penalty in the shoot out as Rovers won 4-2 on spot kicks.
In normal time Rovers missed a penalty and hit the bar in the opening six minutes before Vale struck on the break early in the second half through Robert Taylor. Ash Taylor levelled late on to take the game to penalties in which Owain Fon Williams made a crucial save from Tom Pope.
There were three changes to the side that started against Brentford, with Michael Kay and Joss Labadie coming in for Dave Raven and Andy Robinson and Ash Taylor making his first appearance of the season in place of the rested Ian Goodison. Max Power was named among the substitutes for the first time in 2011-12.
Rovers were almost 1-0 up in less than 15 seconds. After kicking off and playing to the right side of the Port Vale half, the ball fell to Labadie who drilled a right foot shot against the bar from 20 yards, his effort bouncing just in front of the line and away to safety.
Robbie Weir tried his luck from a similar position on three minutes but his effort went high over Chris Martin's bar.
Rovers were awarded a penalty on six minutes for a foul on Tiryaki by Clayton McDonald as he tried to lay the ball off to John Welsh. However, Mark McChrystal stepped up to take the spot kick and smashed his shot against the cross bar with the ball rebounding back into play outside of the area.
After Tiryaki had the ball in the net only for the effort to be ruled out for a foul in the build-up on 13 minutes, McChrystal limped off to be replaced in the centre of defence by Raven.
Louis Dodds registered Vale's first shot on 15 minutes but the effort failed to trouble Owain Fon Williams who caught in front of his chest on his line.
After Martin Devaney dragged a 25 yard shot wide of the target, the second change of the match saw the fourth official and the assistant referee in front of the Johnny King Stand swap places on 18 minutes.
Taylor and Raven combined to cut out an attack up the left from Ryan Burge on 28 minutes, while a Bakayogo cross went straight through the six yard box eight minutes later after the left back was set free by a back heel from Devaney.
The visitors should have taken the lead on 38 minutes when Robert Taylor sent Lewis Haldane through to a one on one with Fon Williams but the striker put his shot past the right hand post under pressure from Ash Taylor.
Tiryaki headed narrowly wide of the far post from a Devaney corner on 43 minutes while the last chance of the half saw Ash Taylor head across goal and wide from Devaney's free kick.
McDonald sent a header straight at Fon Williams in the first minute of the second half and three minutes later the visitors took the lead. A quick counter attack saw Haldane break free of Ash Taylor and though his shot was well saved by Fon Williams, the ball fell straight into the path of Robert Taylor who headed into an empty net from 12 yards.
Haldane almost curled in a second on 53 minutes and Louis Dodds brought a decent save out of Fon Williams six minutes later with a volley from 25 yards.
Robinson replaced Akins on the hour mark, but the attacking midfielder needed treatment soon after when turning awkwardly on the ball. His spell on the pitch lasted just six minutes with Max Power coming on in his place.
A long spell of treatment for Haldane saw the striker eventually carried off on a stretcher needing oxygen. He was replaced by Ben Williamson.
Just when it looked like Rovers' night was over they levelled with three minutes remaining. After Labadie'sfree kick deflected behind for a corner, Devaney's cross was played back across the area and Ash Taylor headed in from close range.
Despite eight minutes of injury time neither team was able to create a clear chance, forcing the game into a penalty shoot out in front of the Kop Stand.
Tranmere (Labadie) 1-0
Port Vale (Roberts) 1-0 hit bar
Tranmere (Power) 2-0
Port Vale (Martin ) 2-1
Tranmere (Welsh) 2-1 saved
Port Vale (Pope) 2-1 saved
Tranmere (Weir) 3-1
Port Vale (McDonald) 3-2
Tranmere (Taylor) 4-2
Tranmere: Fon Williams, Kay, Taylor, McChrystal (Raven 13), Bakayogo, Welsh, Weir, Labadie, Akins (Robinson 60 (Power 66)), Tiryaki, Devaney. Substitutes not used: Coughlin, Buchanan, Raven, Power.
Port Vale: Martin, Yates, Taylor (Pope 90+4), Griffith, McCombe, Owen, Dodds (Roberts 90+4), Burge, Collins, Haldane, McDonald. Substitutes not used: Tomlinson, Morsy, Williamson.
Referee: Mark Heywood
Yellow cards: McCombe (11), Kay (55), Collins (75)
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