The biggest upset over the two days came in Bulgaria, where CSKA 1948 Sofia defeated Spartak Trnava 5-3 on penalties after a second straight 0-0 draw.
In a match littered with yellow cards - there were 12 in total - there were shots on target in a cagey affair. CSKA 1948, participating in just their fourth European tie, held their nerve from the spot, converting all five of their attempts.
Trnava's Marin Lausic was the only one to not score in the shootout, meaning the Slovak side will miss out on group phase football for the third year running. The former European Cup semi-finalists were involved in consecutive draws in Europe for the very first time.
Next for CSKA 1948 will be either Paksi or Panathinaikos, with the latter leading 2-1 from the first leg.
Riga FC were involved in a dramatic match against Vardar Skopje, who had lost the first match 3-2. Taking the lead in the 17th minute, the North Macedonians went down a man moments later, making their task that much more difficult.
Yet, they took the lead in the tie midway through the second half. Trying to hold out for the final quarter of the game, Riga's numerical superiority finally paid off in the 87th minute as Abdulrahman Taiwo made it 4-4 on aggregate.
With extra time required, it was always going to be a challenge for Vardar to keep their Latvian opponents out. The goals flew for Riga in the 30-minute period, scoring four times to win 5-2 at home and 8-4 overall.
Drita also needed extra time in their game, having scored late to deny Floriana a win. It took less than a minute in extra time before the side from Kosovo grabbed their winner via a Kauan own goal. Drita came out on top 2-1 on the night and 3-2 on aggregate to move on.
Tuesday's other Conference League game saw Apollon Limassol defeat Dila Gori 3-0 at home to complete a 7-0 aggregate score.
Kobenhavn find a way through
Wednesday's three matches featured two renowned names in Europe, with FC Kobenhavn given a proper scare against Ukraine's Polissia Zhytomyr.
Mohamed Elyounoussi gave the home side the lead midway through the first half, but they would have to play the second half down a man after Junnosuke Suzuki was sent off for denying a goalscoring opportunity.
For all of the chances they created, Polissia failed to make the most of their opporunity. Robert scored Kobenhavn's second at the hour mark, and they managed to hold on for the last half an hour despite a consolation goal for the visitors. The 2-1 win sent Kobenhavn through 5-4 over the two legs.
In total, Polissia had 26 shots in the 90 minutes, but only four were on target. In contrast, FCK's goals came from their only efforts on target.
Rapid Wien, meanwhile, enjoyed a 6-2 home win against FC Santa Coloma of Andorra. Ercan Kara bagged a hat-trick for the Austrians, who advanced 9-3 overall.
Lugano were also proficient in front of goal, getting past Dukagjini 5-1 in Kosovo to progress 6-1 on aggregate, with Kevin Behrens scoring three of the goals for his side.
The Swiss side return to the round where they were eliminated last summer while scoring the most goals they have ever managed in a European away match.
Thursday will see the second qualifying round come to a close with the other 42 ties to take place.
Keep an eye on everything that happens in UEFA Conference League qualifying on Flashscore.