Otago had a bad end to its day, losing two wickets in as many balls, and will resume today on five for two wickets.
Bowes compiled more than half his side's runs on a day where scoring was not overly brisk.
The former South African under-19 captain scored 152 and batted for almost the whole day, as his side made it through to 287 for nine at its turn at bat.
Otago faced five overs at the end of play, and openers Hamish Rutherford and Brad Wilson were looking solid. But Rutherford was dismissed by Andrew Hazeldine in the penultimate over of the day, and Josh Tasman-Jones was then bowled first ball.
Wilson will resume with Cam Hawkins this morning.
Bowes has a liking for Otago - he scored an unbeaten century in a one day game against the southern side in January this year.
He accumulated rather than dominated on the outer ground at Molyneux Park, bringing up his 100 in 165 balls, though he hit two-thirds of his runs in boundaries on the way to three figures.
He pushed on past 150 and then walked off undefeated with Canterbury at 283 for six.
Otago worked hard all day. Mark Craig, who was captaining the side, took three wickets in the top order, with new wicketkeeper Mitch Renwick picking up a stumping.
Canterbury was struggling at 142 for five, but Bowes got together with Theo van Woerkom and the pair added 76 together.
Hazeldine then chipped in with 35 to help get Canterbury further advanced.
But Christi Viljoen took three wickets in an over to prevent Canterbury from getting 300.
Otago bowled 92 overs, with spinners Craig and Michael Rippon sending down 52 between them.
Craig, who has has a poor injury run in recent seasons, would have been happy to have bowled 30 overs yesterday and gone at just over two an over.
The second day of the three-day game should go ahead today, though occasional rain is forecast this afternoon. Otago will look to bat long into the day to amass time in the middle.
