Izaguirre was carried off on a stretcher early in the game at Pittodrie following what looked a fair sliding challenge from Peter Pawlett.
Celtic struggled to break down the Dons for long periods after that but Kris Commons dispossessed Richard Foster before setting up Stokes to net the only goal of the SPL contest in the 74th minute.
Celtic manager Neil Lennon will not remember this day fondly, though, following the injury to his Honduran left-back, who was the SPL's player of the year last season.
Lennon was already missing three defenders with Glenn Loovens ruled out for up to six weeks with a hamstring injury and Mark Wilson joining Thomas Rogne on the sidelines with a hip problem.
That meant a competitive debut for former Cardiff full-back Adam Matthews while Daniel Majstorovic partnered Kelvin Wilson in the centre.
Celtic, who had played four friendlies since their opening SPL win over Hibernian, began with a 4-1-4-1 formation with Gary Hooper a lone centre-forward and Stokes out wide on the left.
There was an air of trepidation among the home fans as they faced a side who put 21 past them in five games last season after their team began the season without a goal in two games.
However, Aberdeen had an increased resilience to them and Scott Vernon had a couple of decent chances.
Celtic dominated possession throughout though and Commons twice tested home goalkeeper David Gonzalez in the opening stages. Gonzalez first pushed away a powerful 25-yard strike that skimmed off the wet surface and then held the winger's attempted chip.
Celtic were moving the ball around quickly but the hosts were able to occasionally relieve the pressure, mainly because of the pace of Darren Mackie.
Charlie Mulgrew replaced the stricken Izaguirre in the 17th minute and Pawlett was soon booked for a late tackle on the substitute.
Celtic were restricted to long-range efforts in the first half as Aberdeen sat in. Ki Sung-yueng saw one deflected over, Beram Kayal shot just too high after the resulting corner and Gonzales held a Stokes strike after Wilson had brought the ball out of defence.
Celtic were struggling to get round the side of Aberdeen and when Mulgrew managed to get a cross in, Joe Ledley was too far out and under too much pressure to give Gonzalez much concern with his downward header.
Celtic almost fell behind in the closing moments of the half after Stokes gave the ball away. Mackie combined with Scott Vernon on the break and the latter got a shot away just outside the box, but Lukasz Zaluska parried.
Hooper had a shot diverted wide in a crowded penalty box following Ki's injury-time free-kick.
The South Korean glanced a header wide from Matthews' cross 10 minutes into the second half but Celtic were almost caught out when Mackie got away from Majstorovic on the left and whipped in a low cross that Vernon could not turn goalwards from eight yards.
Celtic were getting more men forward when they attacked but could not fashion a clear opening. James Forrest replaced Ledley as Celtic moved to a 4-4-2 with Stokes pushing inside.
Commons soon curled wide from just outside the box but got a free-kick after being caught late by Pawlett's sliding challenge, however Mulgrew could not supply his usual accuracy from the set-piece.
The frustration was becoming audible from the Celtic support and evident among the players too as Kayal lashed a shot high and wide.
But they got the breakthrough after left-back Richard Foster was caught in possession. Commons slid in to take the ball and exchanged passes with Stokes before laying the ball back to the Irishman to sweep into the bottom corner from 10 yards.
Commons cut open the Dons again following a slick move, playing in Forrest, but Gonzalez got enough on the winger's low shot to divert it over the bar.
Celtic were comfortable and substitute Georgios Samaras headed wide Mulgrew's cross.