Shearer faces an uphill task to keep Newcastle in the top-flight following his arrival as manager at the start of April and has now seen his side go eight league games without a win.
Despite seeing the return of Mark Viduka and Obafemi Martins to the Newcastle attack in the second half, they never really looked like taking anything from the game and face a major fight to retain their top-flight status.
The victory for Tottenham keeps alive their hopes of securing a top-seven finish and qualifying for the Europa League next season.
It could have been a different story if Newcastle had opened the scoring after 24 minutes. Ryan Taylor's free-kick caused all kinds of problems for the home defence and Tom Huddlestone's header almost flew past his own keeper as the ball fell inches past the post.
From the resulting corner Kevin Nolan fired his shot straight at Heurelho Gomes.
Newcastle were made to pay as Tottenham raced down the other end and opened the scoring.
Sebastien Bassong failed to deal with a through pass from Luka Modric. The ball fell kindly to Bent who saw his first shot saved by Harper. The England striker made no mistake in placing the rebound into the back of the net.
Tottenham suffered a major injury blow on 31 minutes when Michael Dawson was carried off on a stretcher. He was replaced by Alan Hutton and Vedran Corluka moved into a central defensive position alongside Jonathan Woodgate.
The move didn't seem to affect the home side as Tottenham continued to dominate the proceedings and came close to adding a second on 40 minutes, when Huddlestone fired a blistering 30-yard shot which sailed just over the bar.
Bent could have added his second of the game on the stroke of half-time when Hutton's cross picked him out at the far post, but his header flew just wide of the post.
Shearer was determined to help his side get back into the game and made a bold move on the hour mark when he brought on both Martins and Viduka.
The move almost paid off just sixty seconds later when Viduka backheeled the ball into the path of Martins and he fired over.
Newcastle were now looking a completely different side and Martins fired the ball past Gomes on 67 minutes, but his effort was ruled out after he handled the ball inside the box.
Despite their new attacking threat, Newcastle still looked shaky at the back and Tottenham came within a whisker of adding a second on 69 minutes when Aaron Lennon drilled a low from the edge of the box which flew inches past the post.
Shearer must have known it was not going to be his day when Martins blew another golden chance on 87 minutes when he volleyed over the bar from close range.