Robert Garrett sealed the victory with a goal in a classic counter-attacking move 12 minutes from time.
Thompson redirected Robert Garrett's powerful free-kick past Newry keeper Nathan Morley-Hillen to give the hosts the perfect start.
Robert Garrett, Martin Donnelly, James Lawrie and Shane Ferguson were then handed first caps late in the low-key friendly.
Carling Player of the Month Robert Garrett and Peter Thompson were on target for the Blues at Shamrock Park.
Owens fired wide before Alain Emerson forced the ball in on 68 but Linfield's Robert Garrett then hit the upright.
Blues midfielder Robert Garrett fired over from 16 yards in one of the few chances in a dull first half.
Mikael Lustig saw an effort cleared off the line by Robert Garrett and then Blayney pushed an Annan effort round the post.
Squad regular Alan Mannus is joined by Crusaders pair Colin Coates and Martin Donnelly, Coleraine's Stephen Carson and Linfield midfielder Robert Garrett.
John Connolly scored an 83rd-minute penalty after Marcus Kane tripped Chris Scannell and Robert Garrett was sent-off for a second yellow card after 87.
The first clear goalscoring chance fell to Robert Garrett in the 19th minute but his free-kick clipped the angle of the post and crossbar.
Fellow Irish League players Colin Coates, Martin Donnelly and Robert Garrett are new faces in the panel while Linfield keeper Alan Mannus is a regular in the squad.
Mannus' club colleague Robert Garrett, Martin Donnelly, James Lawrie and Shane Ferguson were also handed first caps late in the game as the Irish continued to battle gamely.
He is one of five Irish League players in the panel, the others being Coleraine winger Stephen Carson, Linfield midfielder Robert Garrett and Crusaders pair Colin Coates and Martin Donnelly.
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