Jed Wallace's free-kick before the interval had given the Lions the lead and it was their fourth consecutive draw.
Millwall had the better of the opening exchanges and their first chance came after three minutes when Ryan Woods received the ball and played in Murray Wallace, who advanced from left midfield, but his shot from 25 yards out was saved comfortably by Rafael.
Yakou Meite looked dangerous and threatened to open the scoring on 23 minutes, driving from the right into a central position and hitting a low shot from 25 yards that deflected towards the bottom right corner, but Bartosz Bialkowski kept it out.
Millwall pressed more towards the end of the first half but a few wayward passes prevented them from finding the final ball to unlock Reading's defence.
Jed Wallace opened the scoring seconds before half-time after Troy Parrott was fouled in a central area 20 yards from goal, stepping up and curling unstoppably past Rafael.
Reading started the second half brightly and looked to get forward with more urgency. Ejaria tested Bialkowski on 50 minutes with a low, curling shot from the edge of the area towards the bottom corner but the keeper held on well.
Joao then equalised for Reading after 53 minutes as the Royals worked the ball through midfield to substitute Michael Olise on the edge of the box.
He released Joao with a flicked through-ball and the striker beat the offside trap and shot through the legs of Bialkowski and into the bottom corner from a tight angle just inside the six-yard box.
Jon Dadi Bodvarsson almost restored Millwall's lead on 68 minutes after Jed Wallace played in the substitute with a first-time pass on the edge of the area. Bodvarsson hit a first-time shot towards the top of the net but Rafael tipped the ball over with a fingertip save.
With 10 minutes left, Ryan Leonard ran from deep and was unmarked inside the six-yard area after Matt Smith knocked down Jed Wallace's cross to the far post but Leonard could not test the keeper and his attempt went over the bar.
Jed Wallace almost scored his second of the evening in added time when Smith ran down the right wing, pulled back from the byline across the penalty box to a sliding Wallace who shot straight at Rafael.