Playmaker Modric, who turned 29, broke the deadlock with a sizzling low shot in the 46th minute and second-half substitute Kramaric capped a fine individual performance with a late goal on his competitive debut.
Croatia's 4-2-3-1 formation looked toothless in the opening half and they failed to create a single chance, even after Malta defender Steve Borg was sent off in the 31st minute for striking lone forward Mario Mandzukic off the ball.
Coach Niko Kovac introduced robust striker Nikica Jelavic for central midfielder Mateo Kovacic at halftime to add bite up front and the substitution paid off immediately after the break.
Modric, making his 80th international appearance, took a half-cleared cross in his stride and unleashed a scorcher through a packed penalty area into the far corner of the net from 25 metres.
Youthful midfielder Alen Halilovic, brought in along with Kramaric after Croatia's group-stage exit in the 2014 World Cup, also went close as the home team upped the tempo.
The skilful Kramaric rattled the crossbar after showing nice footwork in the 70th minute before he sealed victory 11 minutes later with a calm finish after good work by Jelavic and Ivan Rakitic.
"I am overjoyed to have taken three points from this game after a poor first half," Kovac told Croatian television.
"The sending-off of Borg played into our hands and after moving up a gear in the second half with numerical advantage, we were able to break Malta down although they defended very well throughout the match.
"We have some young players who are talented but are yet to gel with the experienced players in this squad and that will take some time," added Kovac.
(Writing by Zoran Milosavljevic, editing by Tony Jimenez)
