Tom Lawrence hit the post with a header on his debut in a disappointing first half for Cardiff, who showed more urgency after the break.
Lawrence and Anthony Pilkington had further chances but MK Dons held firm.
Nicky Maynard wasted a good opportunity for the Dons, who are two points clear of the drop zone.
Cardiff remain ninth in the table, five points off the final play-off spot.
Heavy morning rain in south Wales had put the game in doubt, but the efforts of the Cardiff City Stadium ground staff ensured the match kicked off.
Wales striker Lawrence, signed on loan from Leicester City started while fellow loanee Kenneth Zohore started on the bench.
Dons' new signing Alex Revell was forced to wait for his debut as his contract stipulated he could not face his former club.
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The first half had been a scrappy affair with few chances for either side until Lawrence's glancing header struck the post.
Cardiff finished the first half strongly with David Martin palming away Stuart O'Keefe's header and Peter Whittingham firing over the crossbar.
Martin again denied O'Keefe early in the second half and the Dons keeper tipped Scott Malone's effort over the bar.
Lawrence and Pilkington went close for the home side, who were much improved in the second half.
Former Cardiff City striker Maynard should have given MK Dons the lead, but he fired over after getting the better of Matthew Connolly.
Dons top-scorer Josh Murphy's blocked effort fell kindly for Darren Potter, but the midfielder shot wide.
Bruno Manga headed wide from a corner while at the other end David Marshall, who had little to do all afternoon, made a full length save to deny Jake Forster-Caskey late on.
Cardiff manager Russell Slade:
"We know we still have a good chance of reaching the top six.
"We have lost goals from the team with players being out injured and leaving the club, so we are looking at the players coming in to get them for us.
"We did more than enough to get the three points, but we couldn't quite do it."
Mk Dons manager Karl Robinson:
"We should have had a penalty for a foul on Josh Murphy and I'm sure when the ref sees it again he will agree with me.
"We rode our luck a bit at times and David Martin made some outstanding saves, but I'm proud of the boys.
"It's our eighth clean sheet of the season and is a performance we can really build on."

Cook (65) started strongly alongside opener Nick Browne (60) as the hosts passed a century for the first wicket.
Tom Westley hit a fluent 64 before he was bowled by Ben Sanderson (2-79), who earlier had dismissed Browne.
Ravi Bopara (57 not out) and Dan Lawrence (44 not out) saw Essex to 335-3 at stumps.
Northants also conceded 45 extras, including 28 no-balls.
Cardiff City's play-off hopes suffered a setback after the hosts were held to a goalless draw by Championship strugglers MK Dons.
[NEXT_CONCEPT]
England captain Alastair Cook continued his fine start to the season with a half-century as Essex took control of the first day against Northamptonshire.