Pace bowler Sami was hit on the right knee while at mid-wicket and had to have strapping applied.
It was another worry for Pakistan just days before the opening Test of a four-match series gets underway at Lord's on Thursday.
Pakistan took the field Sunday without fast bowler Mohammad Asif, who had an injection in his right elbow on Saturday and is not exepected to be fit until the eve of the first Test.
And first-choice gloveman Kamran Akmal again did not keep wicket as a precaution after bruising his left index finger on Thursday morning.
Spearhead quick Shoaib Akhtar (ankle) is not in England at the moment while fellow paceman Rana Naved, who has played for English county Sussex this season, is currently struggling with a groin injury.
Meanwhile Pakistan's final first-class match before the Test series was heading towards a draw after rain meant there was only 35 minutes play before lunch on the fourth and final day here Sunday.
England 'A', in the 10 overs that were bowled, added 27 runs to take their second innings score to reach 62 for one, a lead of 415, after they had dismissed Pakistan for 242 in reply to their first innings 595 for nine declared.
Alastair Cook was 26 not out and Ian Bell 17 not out after both batsmen had been included in England's first Test squad announced earlier Sunday.
Left-hander Cook had missed out in the A team's first innings with former England wicket-keeper Chris Read scoring 150 not out and skipper Robert Key, himself an ex-England batsman, 136 while Bell chipped in with a stylish 74.
Then off-spinner Jamie Dalrymple, one of England's few successes in their 5-0 One-day series thrashing by Sri Lanka, took four for 61 - including the prize wicket of Pakistan captain Inzamam-ul-Haq for nought.
But before England took the field Saturday they were without Test regular Matthew Hoggard after the swing bowler had had his right-hand trodden on by Yorkshire colleague Tim Bresnan in a warm-up accident.
Hoggard later had to have six stitches inserted into his bowling hand and on Sunday the selectors called seamer Jon Lewis into the Test squad as cover.