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England thrashed Pakistan by 354 runs in the first of a four-Test series at Trent Bridge last week, although the overcast skies above the Nottingham ground were a boon to swing bowlers on both sides.
Pietersen scratched his way to nine in the first innings but looked to be digging in second time around.
However, he was out for 22 when brilliantly caught off the inside edge by diving Pakistan wicketkeeper Kamran Akmal.
Pietersen has gone 22 innings without a Test century since reaching three figures against the West Indies in Port of Spain in March last year, although that sequence would have been broken had he added just one more run to the 99 he made against Bangladesh in Chittagong in March.
His cause has not been helped by an Achilles injury which forced him to miss most of England's Ashes series win in 2009, and more recently, a thigh problem which meant he arrived at Trent Bridge not having played a match since July 3.
Adding to those difficulties, his announcement he was leaving county side Hampshire at the end of the season has led the south coast club into the unsurprising position of refusing to pick Pietersen even on the rare occasions when he is available.
As a result, the 30-year-old South Africa born shotmaker is having to find his form out in the middle.
But no top four batsman on either side at Trent Bridge made a fifty and Flower said: "Most batsmen looked a little iffy against that swinging ball but it wasn't only swinging -- there was a little movement off the pitch as well.
"Kevin did look better towards the end of the second innings, and that time in the middle is very important for any batsman - so I am glad he spent as long as he did at the crease both for his own good and the good of the team.
"He was one of those who made a contribution up the order. Facing those deliveries in the first innings for 10 overs meant that (Eoin) Morgan and (Paul) Collingwood didn't have to face the swing bowling for those 10 overs - and they were given a lighter load in the afternoon against the spin."
Meanwhile opening batsman Alastair Cook is also in the middle of a lean spell but Flower, speaking ahead of the second Test which starts at Edgbaston on Friday, was confident the Essex left-hander would find his form soon.
"He didn't have a good Test in Nottingham (Cook was out for eight and 12) but he made small contributions.
"In the first innings he put on a partnership of 42 for the first wicket and helped to get us up and running in difficult conditions," former Zimbabwe batsman Flower added.
"The series is only one Test old, Alastair has a great record of performing under pressure and I expect him to do that in the coming games."
