After a summer fighting mumps and then struggling with a calf injury, Owen climbed off the bench to do what he does best by scoring and securing Newcastle's first win of the season.
In 42 appearances for the Magpies, Owen is averaging a goal every two games after heading his second-half winner.
But the home side were also greatly indebted to man-of-the-match Shay Given, who superbly saved a second-half penalty from Kevin Nolan to keep them on level terms.
The opening 45 minutes were instantly forgettable with neither keeper having a save to make as the packed midfield dominated proceedings but created little.
Bolton's cause was not helped when they lost Johan Elmander with a leg injury and Gavin McCann was introduced.
McCann and Joey O'Brien were booked after 39 and 28 minutes respectively, both for crude tackles on Argentinian Jonas Gutierrez.
Newcastle lost Damien Duff at the break and he was replaced by Geremi as the match finally burst to life, with the Cameroon midfielder playing a pivotal part.
Matt Taylor headed over for Bolton and then at the other end, Obafemi Martins lost Gary Cahill only to glance Geremi's right-wing cross wide of the far post.
That was to be Martins' final effort as he appeared to have a thigh injury and Owen was introduced after 53 minutes.
But it was Bolton who were given a golden opportunity to go in front just before the hour mark when they were awarded a penalty following a Steven Taylor handball.
Gretar Steinsson's ball in from the right was flicked on by O'Brien and struck the right hand of Taylor.
Referee Steve Bennett pointed straight to the spot and there was no complaints from any of the United players.
Skipper Nolan was left with the responsibility of taking the kick only to see Given guess correct to his right to parry the shot and kick the rebound clear when still lying on the ground.
Jussi Jaaskelainen pulled off two stunning saves just seconds later to first keep out an Owen header and force Fabricio Coloccini's follow-up behind for a corner.
But United and Owen were not to be denied much longer and charged ahead after 71 minutes.
A James Milner free-kick on the right rebounded straight back to the England Under-21 international who played the ball short to Geremi.
The Cameroon international whipped in a delightful cross and Owen stole in to head downwards and beyond Jaaskelainen.
It should have been all over four minutes later when Habib Beye picked out Milner, who headed over from just ten yards.
Bolton staged a grandstand finish but Newcastle and particularly Given were not to be denied their clean sheet.