Stenny beat Rangers under-20s 3-1 while Turriff's Andrzej Kieczkowski got the only goal against Montrose.
The Fifers' tie with hosts Arbroath went to extra-time but Paul McManus' penalty secured them a 3-2 win.
On Tuesday, Airdrieonians, Albion Rovers, Brechin, Celtic U20, Elgin, Forfar Athletic, Queen's Park, Peterhead and Stranraer all progressed.
At Central Park, on-loan Hearts forward Nikolay Todorov put League Two Cowden ahead but Jack Aitchison levelled for Celtic U20 before Paul Crossan fired the winner, with Chris Turner then sent off for the hosts.
Aberdeen U20 also had a player dismissed, Sam Roscoe red-carded early in their 3-1 defeat by Forfar with Josh Peters netting twice for the visitors.
Andy Jackson scored a brace in Brechin's 4-1 defeat of Cove while Leighton McIntosh completed Peterhead's comeback as they recovered from a two-goal deficit to beat Brora 3-2.
Elgin beat Hearts U20 2-0 and Albion Rovers were winners by the same score against Hamilton U20.
Airdrieonians beat Motherwell U20 while Craig Malcolm netted four of Stranraer's seven goals at home to Spartans, who scored one in reply.
Partick Thistle U20 led Queen's Park through Michael McMullin but John Carter scored on 88 minutes to force extra-time.
The hosts had David Syme sent off before penalties ensued, Gregor Fotheringham netting the decisive kick for the Spiders.
Colin McMenamin and Alan Cook scored for Stenhousemuir against Rangers U20 before Robby McCrorie's own goal and Ryan Hardie's consolation.
Aberdeen U20 1-3 Forfar Athletic
Brechin City 4-1 Cove Rangers
Elgin City 2-0 Hearts U20
Peterhead 3-2 Brora Rangers
Partick Thistle U20 1-1 Queen's Park (aet, 5-6 pens)
Albion Rovers 2-0 Hamilton Academical U20
Cowdenbeath 1-2 Celtic U20
Motherwell U20 1-2 Airdrieonians
Stranraer 7-1 Spartans
Arbroath 2-3 East Fife (aet)
Turriff United 1-0 Montrose
Rangers U20 1-3 Stenhousemuir
Wins for East Fife, Stenhousemuir and Turriff United completed the second round of the Scottish Challenge Cup.