The Dark Blues made a tentative start in Kirkcaldy with Raith’s Lewis Vaughan having the first effort on goal on 17 minutes, but Scott Bain saved easily.
Vaughan tested Bain again before Liam Buchanan brought out another save from the Dundee goalkeeper however it was McCann’s side that came closest to a goal before the break when Randy Walters rattled the bar.
Roarie Deacon went close for Dundee early in the second half with the next action coming on 64 minutes when home striker Greig Spence hit the ground but referee Stephen Finnie ignored appeals for a penalty.
The opener came for Dundee with seven minutes left when recent recruit Sofien Moussa sent a left foot shot home.
Raith levelled when Vaughan drilled home in the last minute however El Bakhtaoui popped up in injury time to convert an Allan pass.
The first game on the new artificial surface at Bayview saw East Fife and Dunfermline fail to hit the net before the Pars won 9-8 on penalties.
The pitch suited the Pars in the first half with Saturday’s four-goal hero Nicky Clark denied twice by Ryan Goodfellow as they dominated.
The second half followed the same pattern however it was Ben Gordon’s missed spot kick that was to prove decisive.
Inverness Caledonian Thistle drew 0-0 at Stirling Albion but grabbed an extra point with a low scoring 2-0 spot-kick success.
In the Angus derby Brechin saw off visitors Forfar 4-3 in the shootout after Isaac Layne crashed in a shot from 20 yards and Mark Millar tied the score in injury time from the spot.
Montrose suffered a second defeat from a Premiership side in four days with Ross County leaving Links Park having enjoyed a 6-0 success. The Gable Endies found themselves a goal down after 15 minutes when Ryan Down picked out Thomas Mikkelsen who headed home.
The Dingwall men doubled their lead on 12 minutes later when Craig Curran converted a penalty after Andrew Davies had been fouled with Michael Gardyne creating a third on 31 minutes when he came off the wing and fired for goal with the home side’s Sean Dillon getting the final touch.
Curran tapped in on the half time whistle, Mikkelsen added his second nine minutes into the restart and Alex Schalk took County’s tally up to six.
Also in Group B Arbroath secured two points after a 1-1 draw at Alloa with a 6-5 win on spot-kicks. The Red Lichties took the lead on 16 minutes when summer signing Blair Yule headed in a cross from David Gold with the Wasps levelling late on through Frank McKeown.
Queen’s Park looked set to create a shock at Morton when they led 2-0 late on however Morton rallied to 2-2 and won the penalty shootout 4-2.
The Hampden side put up dogged resistance in the first half with Willie Muir excelling with stops from Robert Thomson on three occasions.
The Spiders shocked their hosts when Bryan Wharton nodded in with 20 minutes left and 11 minutes later former Morton striker Thomas Orr ran clear to score.
Bob McHugh pulled a goal back with five minutes left and Darren Barr scrambled in an injury time second for the hosts before Gary Harkins hit the winning spot kick.
Edinburgh City got their time as tenants at Ainslie Park off to a winning start with a 4-2 shootout success over Berwick Rangers.
Ashley Grimes sent a low shot home on 23 minutes however Aaron Murrell slid in a leveller seven minutes later. Grimes quickly found the net again to have City leading for a second time with Pat Scullion restoring parity six minutes from time.
In Group G Lowland League Champions East Kilbride earned an extra point at Queen of the South with a 4-1 penalty success after a goalless draw.
Albion Rovers and Stenhousemuir also needed a penalty shoot-out after a 1-1 draw where Colin McMenamin found the Warriors goal on 15 minutes and Alan Trouten equalised with a penalty on 57 minutes. The Ochilview side picked up the extra point with a 3-2 win.
Livingston scored the quickest goal of the night with Dale Carrick firing in a knock down after just two minutes and that was enough to see off the Saints 1-0.
Stranraer went down 3-0 at Airdrie where Diamonds youngster Cameron Russell fired the hosts in front just before the half hour mark.
Andy Ryan notched a penalty in the second half after visiting goalkeeper Cameron Belford was red-carded when he tangled with the striker.
Russell added the third against the ten men with Scott Robertson pulling a goal back before David Barron was also dismissed.