The honour of scoring the first goal at their impressive new ground went to Shrews' centre-back Darran Kempson - who finally broke the deadlock of this hard-fought affair, when he netted early in the second period of extra-time to secure a win the League Two outfit thoroughly deserved.
But hero Kempson almost turned villain, when shortly afterwards he conceded a penalty but the resulting spot-kick was saved superbly by Town goalkeeper Ryan Esson to preserve their lead.
Despite an eye-catching 4-0 opening day triumph at Lincoln, Shrewsbury manager Gary Peters rang the changes and handed first-team debuts to striker Fola Onibuje and on-loan Liverpool midfielder Jimmy Ryan, who joined Shrewsbury for a month earlier in the day.
Colchester were also much-changed from the squad who grabbed a point at Sheffield United at the weekend so it was no surprise the opening stages were tentative.
The closest thing to a breakthrough came in the 19th minute when Shrews' skipper Stewart Drummond saw his header clip the crossbar from a long throw launched into the Colchester area by full-back Marc Tierney - with this route to goal later proving decisive.
Ten minutes before the break Kempson saw a header well-saved by Colchester goalkeeper Dean Gerken but at the other end Esson remained relatively untroubled by the visitors misfiring front-line.
The second half produced some neat play from both sides but neither seriously threatened and when the first half of extra-time went the same way, a penalty shoot out looked the most likely outcome.
But 90 seconds into the second period of extra-time, Kempson rose to glance home a header from Tierney's long throw, which appeared to settle the issue.
Three minutes later, however, Colchester substitute Tom Webb was brought down in the box by Kempson but Esson was equal to John Jackson's penalty-kick to ensure Shrewsbury made a winning start at their new home.