Top-flight Livingston suffered a blow to their hopes of reaching the Scottish League Cup knock-out stage after losing 2-1 to League 1 Alloa Athletic.
The visitors, who had been weakened by Covid-19 infection and illness, lost two goals in the last eight minutes.
Dundee United are all but through after edging out Arbroath 1-0 to secure a third straight group-stage win.
Top-flight Motherwell had to come from two goals down to beat Queen of the South 3-2 for their second in a row.
Dunfermline Athletic recorded the biggest win of the day, thumping Dumbarton 5-1 to move above St Mirren on goal difference at the top of Group H, while League 2 side Stirling Albion held second-tier Inverness Caledonian Thistle away from home before taking the bonus point following the penalty shoot-out.
Striker Bruce Anderson's close-range finish had put Livingston ahead at Indodrill Stadium, but defender Scott Taggart fired Alloa level before prolific midfielder Alan Trouten won it from the penalty spot after Ayo Obileye fouled Cameron O'Donnell.
Cowdenbeath move three points above Livingston and level with Raith Rovers in Group D after striker Kris Renton's second goal of the game with a minute remaining handed the League 2 side a win after Lowland League visitors Brechin City squandered a 2-1 lead and had defender Iain Davidson sent off.
A clever free-kick from former Scotland defender Charlie Mulgrew after 21 minutes was enough to secure victory at Tannadice as Dundee United survived late Arbroath pressure to move three points clear of the second-tier visitors.
Also in Group B, striker Nathan Austin's double helped League 2 newcomers Kelty Hearts to an impressive 3-0 win at home to visitors from the league above, East Fife.
Two goals in the final four minutes of the first half from Queen of the South midfielder Michael Paton, a back-post header followed by 20-yard drive, put Motherwell in trouble at Fir Park.
However, striker Tony Watt slotted a reply for the Premiership side shortly after the break, defender Ricki Lamie headed the equaliser and, two minutes later, summer signing Kaiyne Wollery, the former Tranmere Rovers forward, completed the comeback.
The win lifts Motherwell to the top of Group F, while Queen's Park are two points behind in second despite missing out on the bonus point with a penalty shoot-out defeat by Airdrieonians after a 0-0 draw.
Goals from striker Dylan Mackin and winger Kieran Moore had Stirling 2-0 ahead in Inverness before midfielder Roddy MacGregor fired one back before the break and forward Shane Sutherland equalised.
It leaves Hearts, who were without a game this weekend, two points clear of Caley Thistle in Group A.
Kilmarnock are back in contention in Group G after winning 2-1 away to Clyde having forfeited the points in their opener against East Kilbride for fielding a suspended player, but it is Stranraer at the top after the League 2 side beat East Kilbride 1-0.
Defender Jamie Hamilton late winner against Falkirk lifts Championship side Hamilton Academical above Ayr United and their hosts to the top of Group E.
On-loan Aberdeen midfielder Mark Gallagher's late winner for Forfar Athletic away to Brora Rangers puts the League 2 side two points clear at the top of Group B, although top-flight Dundee have a game in hand.
Scottish League Cup results
Inverness Caledonian Thistle 2-2 Stirling Albion (2-3 on pens)
Peterhead 3-1 Cove Rangers
Dundee United 1-0 Arbroath
Kelty Hearts 3-0 East Fife
Brora Rangers 0-1 Forfar Athletic
Alloa Athletic 2-1 Livingston
Cowdenbeath 3-2 Brechin City
Albion Rovers 1-1 Edinburgh City (5-4 on pens)
Falkirk 1-2 Hamilton Academical
Motherwell 3-2 Queen of the South
Queen's Park 0-0 Airdrieonians (3-4 on pens)
Clyde 1-2 Kilmarnock
Stranraer 1-0 East Kilbride
Dunfermline Athletic 5-1 Dumbarton
Stenhousemuir 1-2 Partick Thistle