Scales are just sets of notes arranged in ascending/descending order. There are many different sets of notes that constitute scales.
The most commonly used in Western music is comprised of seven notes, called the major scale.The gaps between the notes is TTSTTTS, where T=tone and S= semitone. Portrayed conveniently on pianos as the set of white keys, starting with C, the note immediately to the left of the two black keys.
That is really considered the starting point for a lot of theory. The third note in that series is indeed the major 3rd, and to arrive at minor, it's lowered by a semitone.
The pentatonic (major) scale uses notes 1,2,3,5 and 6 of that scale. The pentatonic (minor) scale uses a different set of notes - those from the minor scale. 1,3, 4,5 and 7. hence, in that scale you show on guitar, the notes are A, C, D, E and G.
The major notes in key A are A, B, C♯, D, E, F♯ and G♯. So now, it's clear that the 3rd note from A major is C♯, and gets lowered to C♮ for A minor. Because the min.pent misses out the 2nd note from the full minor scale, its 2nd note is C.