The England striker, with a worried head coach Steve McClaren looking on, suffered his injury blow after an accidental collision with team-mate Matty Pattison midway through the second half left him clearly dazed.
Caretaker boss Nigel Pearson later reported Owen had suffered mild concussion and the injury was not bad enough to keep him out of the forthcoming England B clash with Albania, but it did deny the striker some more valuable game time as he fights his way back to full match fitness following his lengthy lay-off.
The fact that the forward's injury scare was the main post-match talking point said much about what had been witnessed beforehand, but it was Watford who had looked the more likely to make the early breakthrough.
They forced five corners to Newcastle's one in the opening half hour and enjoyed the greater share of possession.
However, it was the managerless Magpies who took the lead against the run of play.
Lee Williamson, who was one of three players to be booked in as many first-half minutes, attempted to cut out Nolberto Solano's precision pass from midfield but failed to make contact and Kieron Dyer raced through to calmly lift the ball over Ben Foster and ruin the departing keeper's hopes of keeping a clean sheet on his Vicarage Road farewell.
But six minutes after the re-start Watford were back on terms.
Adrian Mariappa's cross clearly struck Nicky Butt on the arm and referee Rob Styles had no hesitation in awarding a penalty which Marlon King comfortably tucked away.
After Owen's latest injury blow, Williamson and Douglas Rinaldi could have won it for the Championship-bound Hornets, but there were emotional scenes at the end as newly-crowned player of the season Foster left the field for the final time.
The on-loan Manchester United keeper walked off to rousing chants of 'England's number one' to signal the end of his two-year stay with the Hornets.