O'Neill was livid with his side for their limp display in a 3-2 defeat at lowly Luxembourg last month but has such limited resources that wholesale changes were virtually impossible.
Fit-again Kilmarnock midfielder Sammy Clingan and Bradford defender Rory McArdle have been recalled, while West Brom midfielder Chris Brunt is back from suspension.
Kyle Lafferty, banned after his red card against Portugal, will not be travelling for the matches, which take place in Baku on October 11 and Tel Aviv four days later, while former captain Aaron Hughes is ruled out with a groin problem.
He has not played for Fulham since August 31 and there is a chance he may have played his last international match.
Hughes was tempted out of retirement when O'Neill took the job at the start of 2012 and has given no guarantees he will take on another campaign.
Hughes' absence means Brunt, Jonny Evans, Gareth McAuley and captain Steven Davis are the only Premier League regulars available to O'Neill.
Chris Baird is included after joining Reading but winger Paddy McCourt is again overlooked despite impressing for Barnsley since signing on a free transfer.
Meanwhile, O'Neill, whose contract expires after the qualifying campaign, has confirmed he is in talks with the Irish FA over a new contract, describing the ongoing discussions as 'positive'.
Northern Ireland squad to face Azerbaijan and Israel:
Carroll (Olympiakos), Mannus (St Johnstone), McGovern (Falkirk), McAuley (West Brom), J Evans (Man Utd), Bruce (Hull), Hodson (MK Dons), D Lafferty (Burnley) Cathcart (Blackpool), McArdle (Bradford), Baird (Reading), Davis (Southampton), Norwood (Huddersfield), McGinn (Aberdeen), Ferguson (Birmingham, on loan from Newcastle), C Evans (Blackburn), Brunt (West Brom), Clingan (Kilmarnock), Grigg (Brentford), McKay (Inverness), Paterson (Huddersfield), Ward (Derby), Magennis (Aberdeen).
Azerbaijan v Northern Ireland is live on Sky Sports 3HD on Friday October 11 at 5pm