Ings made his 13th start of the season as he continues to work his way back to full fitness after a lengthy spell out with a knee injury.
The 25-year-old has played just 17 minutes for the Reds’ first team this season, and is likely in his final month with the club before leaving on loan in the January transfer window.
His performance despite defeat in the Premier League Cup will no doubt pique the interest of potential suitors, scoring his sixth and seventh goals of the season.
They were joined by some young hopefuls, too, with George Johnston, Conor Masterson, Herbie Kane and Rhian Brewster all taking to the field at Prenton Park.
And Ovie Ejaria, another player likely to leave on loan in the new year, was deployed in midfield against the young Potters as the U23s looked to improve on their 1-0 loss to Sparta Prague last time out.
Stoke scored their opener after Caoimhin Kelleher made a strong save, with Julien Ngoy steeling in to fire past the Irishman on the rebound.
But Jones, who has been in impressive form for the U23s this season, restored parity, heading home Wilson’s free-kick as the Welshman notched his sixth assist of the campaign.
Tyrese Campbell put Stoke ahead again before the break, before Oliver Shenton made it 3-1 to the visitors on the stroke of half-time.
Ings scored his first of the afternoon after Wilson’s penalty was saved, with the ex-Burnley strike tucking home as he followed through, but Daniel Jarvis maintained Stoke’s lead soon after.
Liverpool scrabbled for a result in the closing stages, but were left rueing a hard-fought loss, with Ings completing his double from the spot after Wilson was brought down.
Substitute Adam Lewis struck twice, while his fellow wing-back Rafa Camacho also scored as Gerrard’s side sealed their 16th win in 23 games since he took over as manager.
The U23s are next in action against their Black Cats counterparts next Sunday in Premier League 2, while Gerrard will lead the U19s into their final UEFA Youth League group clash with Spartak Moscow on Wednesday.
Liverpool U23s: Kelleher; Whelan, Jones, Masterson (Juanma), Johnston (Dhanda); Brannagan, Kane, Ejaria (Alves); Ings, Wilson, Brewster
Subs not used: Williams, Parker