England's victory, achieved inside three days, left them 1-0 up in the four-match series with just two to play.
But with the third Test starting at Leeds's Headingley ground on Friday, Woolmer was adamant fortunes could still turn.
"This is a four match series and you always have a chance to stage a comeback. It is disappointing to lose inside three days. We did not do well with the bat and ball in both the innings and it cost us the match.
"We will come forcefully at Leeds, we have to because the Leeds Test will be very crucial and could decide the series."
Pakistan were skittled out for just 119 on a lively Old Trafford pitch after captain Inzamam-ul-Haq won the toss.
England fast bowler Stephen Harmison, who finished with 11 wickets overall, took six for 19 and from then on in Pakistan were fighting a rearguard action.
Home batsmen Alastair Cook (127) and Ian Bell (106 not out) then made centuries as England piled up 461 for nine declared.
Faced with a daunting task just to make their opponents bat again, Pakistan were bowled out for 222 in their second innings with England left-arm spinner Monty Panesar taking a Test-best five for 72.
"Harmison bowled very well in this Test and we couldn't cope with his bowling in both the innings," former England batsman Woolmer admitted.
"He was the difference and we did not handle his extra bounce," he added after Saturday's close.
But, as in the drawn series opener at Lord's, Pakistan were severely hampered by the loss of leading pace trio Shoaib Akhtar, Mohammad Asif and Rana Naved-ul-Hasan through injury.
Even so, leg-spinner Danish Kaneria (one for 106) was disappointing on a pitch which, as Panesar proved, had plenty in it for the slow bowlers.
"We have not been able to get 10 England wickets (in an innings) in either of the two Tests which shows a weakness in our bowling," Woolmer said.
"The guys have talent but they couldn't deliver. Kaneria had an off Test match but there is no need to panic as he can come back strongly.
"I am disappointed with the way the batting flopped becuase in the recent past we have shown we can fight back."
While Naved has already been ruled out of the tour with a groin problem, Pakistan hope Akhtar and Asif can still play a role in the series.
But former South Africa coach Woolmer stressed: "We will not be hastening the return of any of our bowlers. I can't tell you when Shoaib and Asif will come back."
Meanwhile Andrew Strauss, captaining England in the ongoing absence of the injured Andrew Flintoff, was understandably elated after skippering his team throughout a 5-0 one-day series thrashing by Sri Lanka and at Lord's, where he was criticised for delaying a declaration on the final day.
"This wasn't far off the perfect game to be honest," he said. "If you had to write down on a piece of paper how you wanted to win a Test match, it would have been pretty similar to what went on this week," the opening batsman added.
"I though the bowlers were fantastic, Steve in the first innings especially, but Monty applied some great pressure in both the first and second innings and that was crucial as well.
"And the batters did a really professional, clinical job in compiling a big score. So, all in all, we've achieved all we set out to do in this Test match. "The guys are going to enjoy it but come Friday morning it's nought for nought again and we've got to get back to what we did well here.
"At Lord's we played a lot of good cricket but we didn't have that killer punch. From the first moment in this Test match there was a determination about the guys to deliver that killer punch."