England captain Andrew Strauss said the side would be "better for these three days" after labouring to a three-wicket victory over the ICC Combined Associate and Affiliate XI on Monday.
Against a side made up of players from second tier international teams, the world's top Test side trailed on first innings by 96 and was reduced to 199 for six chasing 261 before scrambling home.
Strauss made a fluent 78 in the run chase but there were second failures in the match for Kevin Pietersen (1) and Eoin Morgan (3).
It took a seventh-wicket partnership of 61 between Steven Davies (37 not out) and Stuart Broad (31) to see England to the brink of success.
The three-day match at the ICC Global Cricket Academy is one of only two England will play ahead of the first of three Tests against Pakistan starting in Dubai on January 17.
"We have seen a lot, experienced a lot and hopefully we can take that into the next game and raise our level against Pakistan A," Strauss told reporters.
"If we are honest then our batting in the first innings should have been better.
"In some ways that was understandable after a long lay-off but there is plenty for us to work on and we are not going to pretend it was perfect by any means," he added.
The final day began with the ICC XI 90 for five, a lead of 186, which was extended to 260 before captain William Porterfield declared at 164 for nine.
Afghanistan's Mohammad Shazhad scored 74, his second half-century of the match, while Broad again impressed with the ball for England, capturing three for 22 to finish with six wickets in his first outing since injuring his right shoulder in September.
Spinner Graeme Swann did not field on the final morning after complaining of tightness in his left thigh, although he did bat towards the end of the match.
Wicketkeeper Matt Prior (bruised finger) and fast bowler Chris Tremlett (eye infection) are both expected to be fit for the next match, a three-day game against a Pakistan Cricket Board XI starting on Wednesday.
However, England will have to do without the services of all-rounder Tim Bresnan, who is returning home after failing to recover from surgery in December to remove floating bone in his right elbow.