Pencil and Brush Tool working mode is similar as they all place anchor points after you draw for best presentation of your freeform line.
The main difference are that brushes can be different type. See below.
Also with pencil tool you can close some open path between any anchors point .
Connect two paths with the Pencil tool
Select both paths (Shift-click or drag around the two with the Selection tool).
Select the Pencil tool (
).
Position the pointer where you want to begin from one path, and start dragging toward the other path. The Pencil tool displays a small merge symbol (
) to indicate you’re adding to the existing path.
Drag onto the endpoint of the other path and release the mouse button.Note:For best results, drag from one path to the other as if you were simply continuing the paths in the direction they were created.
Pencil Tool
The Pencil tool lets you draw open and closed paths as if you were drawing with a pencil on paper. It is most useful for fast sketching or creating a hand-drawn look. Once you draw a path, you can immediately change it if needed.
Anchor points are set down as you draw with the Pencil tool; you do not determine where they are positioned. However, you can adjust them once the path is complete. The number of anchor points set down is determined by the length and complexity of the path and by tolerance settings in the Pencil Tool Preferences dialog box. These settings control how sensitive the Pencil tool is to the movement of your mouse or graphics-tablet stylus.
PaintBrush Tool
Brushes let you stylize the appearance of paths. You can apply brush strokes to existing paths, or you can use the Paintbrush tool to draw a path and apply a brush stroke simultaneously.
There are different types of brushes in Illustrator: calligraphic, scatter, art, pattern, and bristle. You can achieve the following effects using these brushes:
Calligraphic brushes
Create strokes that resemble those drawn with the angled point of a calligraphic pen and are drawn along the center of the path. When you use the Blob Brush tool, you can paint with a calligraphic brush and automatically expand the brush stroke into a fill shape that merges with other filled objects of the same color that intersect or are adjacent in stacking order.
Scatter brushes
Disperse copies of an object (such as a ladybug or a leaf) along the path.
Art brushes
Stretch a brush shape (such as Rough Charcoal) or object shape evenly along the length of the path.
Bristle brush
Create brush strokes with the appearance of a natural brush with bristles.
Pattern brushes
Paint a pattern—made of individual tiles—that repeats along the path. Pattern brushes can include up to five tiles, for the sides, inner corner, outer corner, beginning, and end of the pattern.