The pair have been reunited in Paisley following several seasons together with Dumbarton and a mutual admiration was immediately apparent in the aftermath of a victory which saw the home side come from behind.
Indeed Agnew, who almost marked his competitive debut with a hat-trick, revealed he could not turn down the chance to sign for Murray again.
The 28-year-old midfielder said: “I have a good relationship with the gaffer and although I had offers from other Championship sides it was a no-brainer. I enjoyed working with him at Dumbarton and the style of play we adopted and it’s going to be good here at St Mirren.
“Berwick gave us an early fright but we fought back well and the only thing that could have been better is if I had got my hat-trick. I was pleased with both my goals and I must have made about 15 runs towards the box as I was desperate for another goal but it wasn’t to be. We have a lot of good quality in the squad and although Rangers and Hibernian will be the favourites we can have a good season.”
Blair Henderson shocked St Mirren early on when he completed a lovely passing move with a side-footed finish.
Steven Thompson levelled from the penalty spot on 19 minutes after Robert Wilson was late in tackling Stephen Mallan.
Agnew killed off Berwick’s challenge single-handedly by first firing in a spectacular effort from 20 yards on 50 minutes and then netting with a low drive 11 minutes later.
Saints boss Murray said of the two-goal star: “Scott Agnew has a great left foot and today everything went for him and although that will not happen every day I know what he can do.
“He played many games for me at Dumbarton at Championship level and for me it was a no-brainer signing him.
“Berwick had nothing to lose and scored a goal but I thought we responded magnificently and have come through a tricky tie with some great performances.”
Berwick player-boss Colin Cameron said: “I am pleased with the players because we did well against a team just relegated from the Premier League.”
St Mirren: Ridgers, Naismith, Kelly, Baird, Conlan, Carswell (Howieson 74), Mallan (Goodwin 66), Agnew, McMullan, Morgan, Thompson (McLear 66). Subs Not Used: Cuddihy, Barrowman, Stewart, Wilks.
Berwick: Walker, McNeil, Beveridge, Cameron (Drummond 66), Wilson, Fairbairn, Banjo (Lavery 62), Graham, Henderson, McKenna, Coultress. Subs Not Used: Morris, Russell, R. Graham, Walters.
Ref: A Muir