It was a competitive opening 15 minutes, but the one big chance fell to the away side.
Millwall countered at pace and a pass was put on a plate for Ra'ees Bangura-Williams in space at the back post.
But he let the ball run across his body and side-footed his shot wide of the right-hand post to the dismay of the Lions fans behind the goal.
Portsmouth responded by carving out a decent chance of their own - Josh Murphy's low cross from the left found Colby Bishop but the striker could not get enough contact on his effort.
The ball rebounded to the onrushing Matt Ritchie but his powerful shot was well blocked by Joe Bryan.
Millwall then took the lead just before half-time with a devastating attacking move, Bangura-Williams slotting a beautiful pass in behind the Pompey defence which Ivanovic latched on to.
As Schmid rushed out to stop him, the Serbia international calmly chipped the ball over the keeper and ran off in celebration as it trickled over the line, with the away fans celebrating jubilantly as the ball nestled in the back of the net.
Portsmouth started the second period with intent and pushed the Millwall defence back deeper into their half.
Murphy caused trouble with his pace and trickery down the left-hand side and created a number of opportunities, with Ritchie heading narrowly wide from one dangerous cross.
Pompey dominated the second half but Millwall's most notable chance in the second period came from Aaron Connolly who curled an effort with his right foot just wide of the post from the edge of the area.
The hosts pushed in the final moments that remained, launching long throws into the box but were unable to find a breakthrough - the best chance a header from Bishop that flew just over the crossbar.