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Minwax makes a set of color matched touch up markers for woodworking, you'd have a decent shot of matching the fingerboard better than a stock brown marker. As others said, don't know how well it would hold up long term. If you really want to do it right, the plastic dots could be drilled out and replaced with rosewood. Sounds like a solution in search of a problem, but it's your bass. Minwax Wood Finish Stain Marker - Wood Stain Pen | Minwax
Here's a sticker option, would probably hold up better than marker, color match a crapshoot.
A more serious method would be to pull the inlays and tidy up the holes the inlays sit in. Take a junk rosewood neck or rosewood scrap and a plug cutter of the correct diameter and make some rosewood plugs to fill the dots. Glue the plugs in and fill any gaps with rosewood dust + glue. Level the new rosewood inlays carefully and then stain the fretboard a uniform subtly darker shade. Feed the board with lemon oil or your board oil of choice.
If I were to use such a marker I would probably follow it with an application of Stewmac's Fretboard Finishing Oil to act as a protective barrier and to slightly darken the rosewood so the marker isn't so obvious.
First what kinda dots are they? MOP, Abalone, or Turquoise won't hold it well at all. Clay dots should hold the color rather well, your problem there would be color match.