Blues can't find a breakthrough
Michael Drennan replaced Patrick Agyemang up front, while Dan Butler made way for Nicky Shorey on the left.
The best chances came at the death as Jed Wallace and Ryan Brunt both came close to grabbing a winner for their team.
Both sides struggled to find any attacking fluency in a game where the goalkeepers had a largely quiet afternoon.
Pompey drew for the third successive weekend with a goalless stalemate at Bootham Crescent.
York 0 Pompey 0 Half Time:
But the Minstermen had the final say in stoppage-time, only for substitute Jake Hyde to scuff his shot after being teed-up by Lindon Meikle.
Pompey, meanwhile, finished the half with a flourish and a couple of fluid attacks had to be scrambled to safety.
But the home fans thought they should have a penalty when Ertl grappled with Wes Fletcher in the box, only for referee Geoff Eltringham to wave away their appeals.
Paul Jones was having a quiet afternoon in the Blues goal, although he did make a couple of regulation stops to keep out long-range efforts from McCoy and Femi Ilesanmi.
But Pompey were forced into a change midway through the first half when Whatmough limped off to be replaced by Johnny Ertl.
Another set-piece caused York problems on 17 minutes, with Craig Westcarr picking out an unmarked Danny Hollands to drill inches past the post.
A corner was then only cleared as far as Jack Whatmough on the edge of the box, but the defender’s low drive was blocked by a well-placed Marvin McCoy.
The visitors did improve as the match wore on, however, and Wallace was not too far away from connecting with Drennan’s low ball into the box.
Pompey were slow out of the traps and almost punished when Michael Coulson guided Ryan Jarvis’ cross narrowly off target.
The second half started at a leisurely pace, with neither side looking particularly threatening going forward.
A neat free-kick routine did present an opening for Pompey on 54 minutes, but the move ended with James Dunne volleying over.
Lewis Montrose then came close to breaking the deadlock after meeting McCoy’s cross just past the hour mark, but his header drifted narrowly over the crossbar.
At the other end, Jones did well beat away a fierce drive from Jarvis as the Minstermen began to pick up the pace.
Ryan Taylor had made a goalscoring comeback from injury for the reserves during the week and replaced Drennan on 69 minutes.
The full-back was shown a yellow card and Shorey stepped up to curl the free-kick inches past the post.
Pompey were struggling to make any attacking inroads, although they were handed a decent opportunity when a rampaging Wallace was felled by Ilesanmi.
Westcarr then twice failed to connect as he attempted an over-head kick and a header before being withdrawn for Nigel Atangana.
It was the hosts who almost scored soon after, though, with Paul Robinson making a brave block to intercept Hyde’s fierce effort.
Pompey almost snatched a winner late on, but Wallace was denied by York keeper Michael Ingham before sending the loose ball wide.
Ingham; McCoy, Lowe, McCombe, Ilesanmi; Jarvis (Platt 90), Montrose, Penn (c), Coulson (Meikle 4); Fletcher (Hyde 43), Brunt York (4-4-2):
Brunt missed the best opportunity at the other end in stoppage-time, though, somehow contriving to send a free header wide from just a few yards out.
Jones; Devera, Robinson, Whatmough (Ertl 22); Wynter, Wallace, Dunne, Hollands (c), Shorey; Westcarr (Atangana 80), Drennan (Taylor 69) Pompey (3-5-2):
Mooney, Straker, Summerfield, Hirst Subs not used:
McCombe, Ilesanmi, Penn Booked: 3,857 (984 Pompey fans)Attendance:
Geoff Eltringham Referee:
Poke, Webster, Barcham, Holmes Subs not used:
Hollands Booked: