The 22-year-old left-hander tucked paceman Nuwan Pradeep for a single to reach his third test century when a draw was agreed upon by the two sides with Bangladesh on 271 for three wickets, still 196 runs behind an improbable victory target.
Sri Lanka had won the first test in Dhaka by an innings and 248 runs.
Resuming on 12 for no loss, Bangladesh openers Tamim Iqbal (31) and Shamsur Rahman (45) denied the Sri Lankans any early breakthrough and went on to raise 71 runs.
Tamim was the first to go, bowled by part-time leg-spinner Kithuruwan Vithanage, while first-innings centurion Shamsur departed soon after, his defence breached by off-spinner Dilruwan Perera.
Number three batsman Imrul Kayes, who made 115 in the first innings, added 70 runs for the third wicket with Mominul to resist Sri Lanka's push for a victory.
Perera dismissed Kayes (25) leg before in the afternoon session for his second wicket of the innings.
Mominul, who hit 11 boundaries during his 192-minute vigil, combined with experienced all-rounder Shakib Al Hasan (43 not out) in an unbroken stand of 120 runs to snuff out Sri Lanka's hopes of a victory.
