Christchurch went ahead in the 20th minute but Callum Overton, who scored 15 goals in eight appearances for the U23s after a long-term injury lay-off, pulled Chi back into the match four minutes later.
Overton, Ethan Prichard and Flori Vucay were three changes to the starting XI that lined up against Baffins Milton Rovers last time out.
In a competitive, and at times feisty, opening 45 it was the visitors that forged the first opportunity seconds in when an attempt straight from the kick off almost caught out a back-peddaling Mowthorpe only to land on the roof of the net.
Emmett Dunn then headed wide as Vucay nodded the first corner back into the box in the ninth minute.
Next Vucay was brought down under a heavy challenge in the penalty area after Ryan Davidson picked him out with a super pass but the referee waved away Chi appeals.
Kaleem Haitham, who scored the lone goal of the match against Baffins, forced a smart save out of the Christchurch No1 on the quarter hour mark before Matt Axell stung the keeper’s gloves with a fierce effort.
The visitors then got in far too easily and took the lead with a nice finish capitalising on a defence splitting pass.
Overton equalised in Chi’s next attack as things heated up.
Following a bit of handbags and a subsequent stand-off between Dunn and a Christchurch player the ref called over both captains for a talking to.
Haitham then combined with Overton whose shot was saved this time just before Prichard went close from distance when space opened up for him.
A well-timed tackle by Lewis Hyde instigated a slick move involving Dunn, Axell and Davidson but it broke down in the final third.
Christchurch won a corner as the ball ricocheted off a Chi defender which was blocked.
The hosts got away and Overton was fouled on the edge of the area. Axell stepped up and lifted his set-piece narrowly over the bar.
And at the other end Mowthorpe pulled off a fine stop on the stroke of half time to keep it all square heading into the break.
Lloyd Rowlatt, Jamie Horncastle and Ben Pashley were introduced and the home side created a decent early opportunity after Prichard broke down the right flank and found Haitham with a cross the No11 failed to connect with.
The City youngster was involved again moments later when Horncastle sent him away this time but Overton fouled the keeper looking to latch on to Prichard’s delivery.
Prichard, who threatened regularly in the second period, had a strong shot on the turn that was somehow palmed over and a diving header denied either side of the hour.
Christchurch then flashed an attempt wide before Dan Wood saw a decent effort saved.
U18s Ollie Barry and Joe Masters came on for Overton and Prichard with 15 to go.
Good work from Dunn and Rowlatt set Theo Bennetts up for a strike, Rowlatt dragged one wide and Haitham fired an attempt over the bar with the hosts in control.
The visitors though might have nicked it seven minutes from time but a smash and grab effort fizzed inches past the post before Chi conceded a corner late on that came to nothing following a poor back pass.
So, the game went straight to penalties.
Haitham’s first penalty was saved and the away side blazed the subsequent one over the bar.
Pashley, Rowlatt, Corey Heath, Connor Cody, along with their Christchurch counterparts, all converted pens, as did Horncastle and the visitors’ first sudden death penalty taker.
Bennetts coolly made it 6-5 to Chi and Mowthorpe, who saved a couple in the FA Cup preliminary qualifying round shoot-out against Basingstoke last September, pulled off a fine stop to earn Chichester the trophy in dramatic circumstances.
Danny Potter, in the dugout with fellow coach Darin Killpartrick and assistant manager Graeme Gee, said, “Playing Christchurch in pre-season is one of our special games. Last season we couldn’t play them for obvious reasons. It was great to host them this year. They’ve got a very new squad. It was nice to welcome Tony and Jacques Bernard to Oaklands Park, which they haven’t been to for a few years, along with friends of the Steve Bernard Foundation as well.
“It was a very competitive end to end game. Full credit to Christchurch, their management staff and players for putting in a real shift. We were very impressed by their desire to be in the game and they did well to go in front. They took their goal well.
“We’ve got a few things to work on in terms of our personnel and what we want to be doing and how we start the season.
“We were pleased with how we responded and it was great to welcome Callum Overton back to the team. He was vitally important and he took his goal in real style.
“We’re not going to over-play him straight away because he’s missed a number of weeks.
“It was also good to mix up the line-up. Flo started again and did very well, Matt Axell played in a more advanced position and Ben Pashley, who’s done so well for us the past few seasons, came on in the second half and played 45 minutes.
“We’re focused on what we’re going to be doing next. We’ve got a tough game against Basingstoke on Saturday and then we head over to Bognor on the 7th August.
“We’re not getting carried away – we’ve won on penalties here thanks to a good save from Mowey at the end and just about got over the line. We should have maybe done it in the 90 but showed a bit of character.”
Chi welcome Basingstoke to Oaklands Park on Saturday 31st July (Kick Off 1:00pm).
Chichester – Mowthorpe, Davidson, Hutchings, Axell, Cody, Hyde, Prichard, Vucay, Overton, Dunn, Haitham. Subs: (Heath, Wood, Pashley, Rowlatt, Bennetts, Masters, Barry)