The former Ross County and Dunfermline boss, who won the League Cup with County in 2016, replaces Neil McCann, who left his position at Dens Park on Tuesday.
Dundee are bottom of the Scottish Premier League, a point behind St Mirren, after eight games.
"Jim joins on a one year rolling contract and will meet the players tomorrow morning before taking training", an official statement confirmed.
"46 year old, Jim has enjoyed a successful managerial career over the past 10 years with time in charge at Dunfermline Athletic, Queen of the South and Ross County".
Forward Kenny Miller, who joined Dundee in August, told 'BBC Radio Scotland' that McIntyre is coming in to a "fully committed dressing room and fantastic working environment".
He added: "Whoever it was that came in was going to have a very, very good group of players, a group of players that just need a wee lift, a wee bit of confidence.
"There's no doubt in my mind that we will turn the corner sooner rather than later. We've got a huge game on Saturday."