Artur Jorge's men were seconds away from taking a two-goal lead to Athens, but a last-gasp response from Panathinaikos has the Greek giants in with a strong chance at salvation.
Match preview
With a full eight days to rest and recuperate from their thrilling penalty-shootout triumph over Marseille in round three, Panathinaikos had little to fear when they met Braga at Estadio Municipal, and Ivan Jovanovic's men managed to keep their hosts at bay until the half-time whistle sounded.
However, the Shamrock's defensive resilience was eventually broken through Abel Ruiz before Alvaro Djalo doubled Braga's advantage, but with five minutes of injury time on the clock, Daniel Mancini came up with a potentially priceless response to reduce the arrears.
Panathinaikos will not benefit from the abolished away goals rule on Tuesday night, but Jovanovic's side are not down-and-out by any means, and a comprehensive 3-0 Greek Super League win over Volos at the weekend served as the perfect warm-up to their imminent continental contest.
Adam Gnezda Cerin, Fotis Ioannidis and Benjamin Verbic's strikes ensured that Panathinaikos would kick off their new domestic campaign on the right foot, and it is now 12 games without defeat for the Shamrock at their Athens headquarters since a 3-0 beating at the hands of PAOK in January.
By successfully overturning their first-leg deficit, Panathinaikos would enter the draw for the Champions League group stage for the first time since the 2010-11 campaign, but even if Jovanovic's side cannot upset the odds, a return to Europa League football after a seven-year absence would still represent considerable progress.
In contrast, Braga have regularly emerged onto the field to the Europa League anthem on Thursday nights - taking part in the continent's secondary tournament in each of the last four seasons - but a Champions League homecoming is now within touching distance.
Jorge's side made light work of Serbian foes Backa Topola in the third qualifying round with a crushing 7-1 aggregate victory, while they also recovered from a sticky start to their Primeira Liga campaign before overcoming Panathinaikos last week, defeating Chaves 4-2 away from home.
While their upcoming foes did have domestic matters to concern themselves with at the weekend, Braga have been blessed with a hiatus from Primeira Liga action to prepare for a taxing trip to Athens, where history will also be on their side.
Indeed, the Archbishops' only two Champions League proper appearances so far have come from the qualifying path, as they overcame Sevilla 5-3 over two legs at this stage in 2010, two years before a tense penalty-shootout win over Udinese, although the less said about their group-stage records on both occasions the better.
Panathinaikos Champions League form:
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Panathinaikos form (all competitions):
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Braga Champions League form:
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Braga form (all competitions):
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Team News
With no injury concerns arising from their first-leg loss, Panathinaikos boss Jovanovic had the luxury of making several alterations for their league opener at the weekend, where his team also emerged unscathed on the fitness front.
While Verbic and Mancini have both made the net bulge for their side over the past week, fellow attacker Sebastian Palacios was withdrawn before the end against Braga and Volos without directly contributing to a goal, and his spot in the team may therefore come under serious threat.
Ioannidis has also made a strong case to displace Andraz Sporar at the tip of the attack, and a recall to the number 10 role should be in order for Filip Djuricic, as ex-Everton winger Bernard returns to substitute duty.
On the other hand, Braga boss Jorge was forced into an unwanted early substitution in last week's first leg, as midfield screen Al-Musrati lasted just 36 minutes before having to be replaced, having apparently suffered a foot sprain following a tackle.
At the time of writing, the severity of the Libyan's problem is yet to be confirmed, and it remains to be seen whether he will be able to travel to Athens with his teammates, so Andre Horta could instead form the double pivot with Vitor Carvalho.
The former's brother - long-serving attacker and captain Ricardo Horta - set up both of Braga's goals in the first leg to take his assist tally to four in the Champions League qualifying rounds, but the 28-year-old is still waiting for his first strike at the elite European level.
Panathinaikos possible starting lineup:
Brignoli; Vagiannidis, Jedvaj, Magnusson, Juankar; Vilhena, Perez; Verbic, Djuricic, Mancini; Ioannidis
Braga possible starting lineup:
Matheus; Gomez, Fonte, Niakate, Marin; A. Horta, Carvalho; R. Horta, Bruma, Djalo; Ruiz
We say: Panathinaikos 1-1 Braga (Braga win 3-2 on aggregate)
Needing to cling onto a slender advantage at a stadium where Panathinaikos are seldom outclassed, an injury to Al-Musrati is exactly what the doctor did not order for Braga, who may have to adopt a more cautious approach if the Libyan is not passed fit.