After an entertaining first half where both goalkeepers were regularly called into action, Sheffield Wednesday broke the deadlock seven minutes after the interval through Clinton Morrison.
Wednesday appeared to be holding out in relative comfort until Danny Batth brought down Gary Taylor-Fletcher in the first minute of stoppage time.
Veteran striker Phillips made no mistake to ensure Ian Holloway's npower Championship side will get another crack at their League One opponents, who dumped them out of the Carling Cup on penalties in August.
Both side made eight changes as Keith Southern returned to the Blackpool midfield for the first time since having surgery to remove a testicular tumour in November.
Holloway's men went on the attack from the off with the backing of a fervent full-house.
Full-back Robert Harris narrowly missed out with a pair of strikes from distance while Matt Phillips brought a save out of Wednesday goalkeeper Stephen Bywater with a low drive.
The visitors responded through Ryan Lowe, who stabbed wide from close range before drawing a sharp parry from Matt Gilks in the Blackpool goal.
Gilks bettered his previous effort to thwart a curling Lowe effort that was destined for the top corner in the 23rd minute.
Shortly after the half hour, Blackpool were back on the front foot and Kevin Phillips arched an effort inches wide after cleverly engineering space.
Southern's return almost turned sour when a header back towards his own goal fell short to present Clinton Morrison with an opportunity, but Gilks was again equal to the task.
Bywater proved their were two goalkeepers in inspired form on the stroke of half-time as he somehow thwarted Billy Clarke from point-blank range after Matt Phillips burst down the right.
Following a quiet start to the second period, Wednesday went ahead in the 52nd minute.
David Prutton's through ball found Lowe, who tried to round Gilks but had the ball touched away from him, presenting Morrison with the chance to finish clinically from an acute angle.
Nouha Dicko, a surprise loan signing from Oldham, came on for Clarke to make his Blackpool debut and flicked a cross from fellow substitute Gary Taylor-Fletcher goalwards, but the Seasiders were struggling to fashion clear opportunities.
Tom Ince was also introduced to leave the hosts with five forwards on the pitch in the closing stages.
It appeared their efforts would be in vain until, in stoppage time, Batth hauled down Taylor-Fletcher in the area and Phillips thumped home from the spot.