Sampson headed home a Jamie Devitt cross from close range four minutes into added time to deny the Iron three points, which would have moved them on to the cusp of promotion.
Russ Wilcox extended his unbeaten run as boss to 27 games with a solid performance to take his side a step closer to silverware.
Top scorer Sam Winnall opened the scoring on 22 minutes with a close range header. Paddy Madden was the provider with a pinpoint cross from the right and Winnall's downward effort evaded the flat-footed Barry Roche.
The Iron went were denied a second two minutes later when David Syers's header from a left wing corner beat Roche but was cleared off the line by Alex Kenyon.
Morecambe dominated the second half but were denied on two occasions by Sam Slocombe who tipped away a Ryan Williams free kick before showing brilliant reactions to block a well struck Jack Redshaw volley.
But there was nothing the goalkeeper could have done about Sampson's late header.