Holloway, who took over from Pulis at Home Park in the summer, has been laid low with the flu this week but made it to the bench to see the Pilgrims take the lead through Sylvan Ebanks-Blake's 40th-minute penalty.
However, the FA Cup quarter-finalists' lead lasted just 15 minutes as Stoke, revitalised by substitute Lee Martin equalised through midfielder Darel Russell's close-range shot.
Holloway had dropped suspension-threatened David Norris from the Pilgrims' starting line-up in order to guarantee the midfielder's participation in next weekend's last-eight clash with Watford.
Pulis, who left Argyle to return to Stoke having guided the Pilgrims to 14th place in the Championship last term, was booed by Plymouth fans before his side wasted a good opportunity when Mamaday Sidibe headed Lee Hendrie's cross wide from just two yards out.
A reflex save from Stoke goalkeeper Steve Simonsen denied Argyle's Hungarian international winger Peter Halmosi before the Potters' Belgian defender Carl Hoefkens tripped Halmosi for a penalty.
Ebanks-Blake smashed the ball past Simonsen to register his fifth goal of the season.
Argyle's Dutch defender Marcel Seip cleared off the line after Sidibe had taken the ball around Pilgrims goalkeeper Luke McCormick.
Simonsen denied Kevin Gallen from Luke Summerfield's cross before Hendrie limped out of the action to be replaced by on-loan Manchester United winger Martin.
Gallen also missed a great opportunity to finish off the game when he was sent clean through. However, a combination of Simonsen and substitute defender Carl Dickinson thwarted him.
Martin then found John Eustace following a penetrating run down the Argyle right, and the latter's pass was slammed into the net by Russell.
A draw was the right result on the day but Stoke should have nicked all three points in the third of three minutes of stoppage time when Salif Diao headed Martin's free-kick straight at McCormick.