Chandimal's overnight partner Dhananjaya de Silva advanced from 116 to 129 before falling in the first hour, but not before the pair had rescued the innings with a 211-run partnership for the sixth wicket after coming together with Sri Lanka at 26 for five.
Chandimal, scoring his seventh Test ton, remained unbeaten on 105 at the break with strong support from Rangana Herath on 14.
Chandimal and de Silva started the second day cautiously, playing out three straight maiden overs, but soon gained momentum after hitting a couple of boundaries.
Lyon, rewarded for his persistence, pitched the ball outside the off-stump, with de Silva nicking the ball to Shaun Marsh at short leg.
The 24-year-old, playing in only his third Test for Sri Lanka, was given a loud ovation by the home crowd as he left the Sinhalese Sports Club (SSC) ground.
An undeterred Chandimal continued to frustrate the Australian bowlers with some aggressive strokeplay.
The wicketkeeper-batsman's signalled his intent with a six off Lyon on a reverse sweep and he continued to score regular boundaries.
However soon after, Chandimal survived a dropped chance at first slip by Australia skipper Steven Smith with left-arm spinner Jon Holland the unlucky bowler.
Australian pace spearhead Mitchell Starc and Lyon, who wreaked havoc in Sri Lanka's top order on Saturday, have taken three wickets each.
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