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With England looking for an opener to partner Alastair Cook, Moeen was out for seven and 12 against Pakistan A as the tourists batted through the day in Sharjah regardless of wickets lost.
Alex Hales was out for nine, while Jonny Bairstow and Ben Stokes both fell for nought as England mustered 198-11.
James Taylor impressed with 61 after initially retiring for 45.
Ian Bell also retired at lunch for 53, with captain Alastair Cook and vice-captain Joe Root not batting after spending time in the middle during the first warm-up.
Pakistan A had posted 192 for the loss of 12 wickets on day one, so while the match is officially classed as a draw, the result was rendered meaningless by an arrangement that saw both sides bat for a day each.
However, meaning can certainly be attached to the failures of Moeen and Hales as England look to install Cook's seventh opening partner since Andrew Strauss retired in 2012.
Moeen, still most likely to open in the first Test in Abu Dhabi starting on Tuesday, followed his 22 in the first warm-up game earlier in the week by edging to second slip, then returning later in the day to be trapped lbw.
Hales, in his first innings of the tour, was unable to capitalise on Moeen's struggle as a flat-footed drive saw him edge to first slip, the first of four wickets for left-arm seamer Mir Hamza.
Taylor, also featuring for the first time on the tour, pressed his claim, but still seems unlikely to displace Bairstow, who made 66 in the opening Tour match, in the middle order.
Wicketkeeper Jos Buttler spent some much-needed time in the middle, albeit in his second innings of the day, with 39, but Stokes has made only six runs across the two warm-up matches.
"Moeen and Hales got off the mark comfortably in the first over, but after that both were unconvincing. Moeen had several wafts outside the off stump and, two balls before he was out, edged through the slips.
"After he was held at second slip off Junaid Khan, all eyes were on Hales, but he edged with a flat-footed drive. Moeen walked off holding his helmet in his hands, while Hales looked in the direction of the press box. Both realised it was an opportunity missed."
Moeen Ali was out twice on the final day of England's last warm-up match before the first Test against Pakistan.