The Sri Lankan captain hammered an exact 100 off 105 balls with 13 fours to help his team overtake Pakistan's total of 300 with five balls to spare in a tense finish at the Eden Gardens on Tuesday.
Sri Lanka successfully chased the same target against India in the opening match on Monday, with left-handed Arnold (96 not out) playing a big role.
Arnold, who represented the national team in Test matches and One-day Internationals, received valuable support from opener Shantha Kalavitigoda who scored 74 off 96 balls with one six and 10 fours.
Pakistan 'A' skipper Shahid Afridi put his team on course for a challenging total with a brisk 47-ball 63 which contained two sixes and eight fours.
Middle-order batsmen Bilal Asad (52 not out) and Faisal Iaqbal (50) then built on their captain's knock, but their team still failed to stop Sri Lanka from posting the second successive win.
Left-arm spinner Ranga Herath was the most successful Sri Lankan bowler, finishing with 3-52 off 10 overs.
Pakistan 'A' will meet India 'A' in the next match on Thursday.
Pakistan 'A' 300 in 49.5 overs (Shahid Afridi 63, Bilal Asad 52 not out, Faisal Iqbal 50, Salman Butt 29, Mohammad Hafeez 28, Ranga Herath 3-52, Nuwan Kulasekara 2-65, Tharanga Lakshitha 2-68) beat Sri Lanka 'A' 304-5 in 49.1 overs (Russel Arnold 100 not out, Shantha Kalavitigoda 74, Jehan Mubarak 42, Naveed Nawaz 24, Shahid Afridi 2-56, Mohammad Hafeez 2-46) by five wickets.
Man of the Match: Russel Arnold (SRI).