Craig Harrison lost on his return to Connah's Quay Nomads as new side The New Saints were knocked out of the Nathaniel MG Cup.
Michael Wilde gave holders Nomads a 34th minute lead but Declan McManus levelled with 11 minutes left.
Both sides missed penalties in the shoot-out before Ryan Harrington's successful kick secured a 5-4 win for Nomads and a place in the third round.
Harrison left Nomads earlier in the week to return to TNS.
Nomads appointed former Prestatyn and Flint boss Neil Gibson as Harrison's successor.
In Saturday's other second round ties Aberystwyth Town beat Llanidloes Town of the Cymru North 2-1 while Cymru Premier newcomers Pontypridd United beat Carmarthen Town 2-0.
Sunday's ties saw Gresford Athletic of the Cymru North beat Airbus UK 2-1, Cardiff Met were 2-1 winners over Newtown while Bala Town won 6-1 at Chirk AAA.
Haverfordwest County and Caernarfon Town are through after wins over tier two opposition on Friday evening.
Iwan Cartwright scored the only goal of the game as Caernarfon were 1-0 winners at Holyhead Hostpur, who had been reinstated in the competition after Llandudno were removed.
Tony Pennock won his first match in charge of Haverfordwest, as they beat Barry Town 4-2.
Buckley Town won 1-0 at fellow Cymru North side Cefn Druids and Afan Lifo beat Cwmbran Celtic 5-2.
With Penybont receiving a bye into the third round, the final tie of the second round on Tuiesday evening saw Colwyn Bay of the Cymru North beat Cymru Premier Flint Town United on penalties.
But the Bay have been removed from the competition for not including an academy players among the four substitutions they made during the game.
It is the same rule which saw a number of clubs removed from the competition in the first round.
Friday, 5 August
Afan Lido 5-2 Cwmbran Celtic
Cefn Druids 0-1 Buckley Town
Haverfordwest Country 4-2 Barry Town United
Holyhead Hotspur 0-1 Caernarfon Town
Saturday, 6 August
Caersws 1-6 Holywell Town
Connah's Quay Nomads 1-1 The New Saints (Connah's Quay won 5-4 on penalties)
Guilsfield 0-1 Ruthin Town
Aberystwyth Town 2-1 Llanidloes Town
Pontypridd United 2-0 Carmarthen Town
Trefelin BGC 0-5 Taffs Well
Ammanford 2-1 Swansea University
Sunday, 7 August
Gresford Athletic 2-1 Airbus UK Broughton
Chirk AAA 1-6 Bala Town
Cardiff Met 2-1 Newtown
Tuesday, 9 August
Colwyn Bay 1-1 Flint Town United (Colwyn Bay won 5-4 on penalties)