Boro, expected to name Gareth Southgate's successor on Monday, were on course for their fifth away win in the league this season after goals from Gary O'Neil and Adam Johnson.
Paul Parry briefly brought Preston level; then Jones equalised for a second time in the second minute of stoppage time to deny Colin Cooper victory in what will probably be his only game as caretaker manager.
Boro started brightly - and only timely challenges from Neill Collins and Liam Chilvers, both to thwart Leroy Lita, stopped them taking an early lead.
Adam Johnson, who scored the goals against Derby in midweek, then went close with a shot from the edge of the area.
Only a superb save from Andy Lonergan kept Boro at bay after 15 minutes. O'Neil's 30-yard free-kick looked to be heading into the top corner, but the Preston goalkeeper managed to push the ball round the post.
That sprung Preston into life, and Ross Wallace narrowly missed the target with a long-range effort.
Parry should have done better after dispossessing Joe Bennett on the edge of the box.
Lita shot over the bar just after the half-hour, but Boro's dominance was rewarded two minutes before the break.
O'Neil was fouled by Parry 25 yards out. The former Portsmouth midfielder took the free-kick himself and thundered a shot through the wall and into the bottom corner, giving Lonergan no chance.
Boro could have extended their lead before the break when Johnson broke clear down the right. The England Under-21s international had Lita supporting him in the box - but rather than pass, he shot wide from a tight angle.
It looked an even worse decision when Preston equalised just after the hour.
Brad Jones did well to keep out Jon Parkin's header. But the Boro defence could not clear the ball, and it fell to Parry - who could not miss from six yards.
However, Preston's parity was short-lived - and Johnson scored
his third goal of the week, sweeping home Lita's left-wing cross in the 67th minute.
Rhys Williams almost put the game beyond Preston when his well-struck shot from the edge of the box struck a post.
It proved a lifeline for the hosts as Jones rescued a point for Preston, heading in Wallace's cross from close range.