Unai Emery's Arsenal hold a healthy advantage going into next week's second leg thanks to a fine early strike from Juventus-bound Aaron Ramsey and an unfortunate Kalidou Koulibaly own goal midway through the first half, and can rue missed chances that would have put the tie completely beyond the Italians' reach.
"To keep a clean sheet and score a couple of goals is a lovely way to start the first leg. We're delighted with that," said Ramsey, who should have added the third when he blazed over with nine minutes left, to BT Sport.
"We can go into the second leg with a little bit of a cushion, but we know it will be a difficult place to go... They are a quality team."
Chelsea meanwhile escaped from Eden Arena after a bitty display that saw Kepa Arrizabalaga have to make some fine saves to keep the Czechs out before Alonso nodded home Willian's pinpoint cross four minutes from time to seal a 1-0 win.
The Blues remain unbeaten in the Europa League, keeping eight clean sheets in the competition this season, and it was that solidity that saw them through on a tricky evening in Prague.
The Premier League pair remain on a collision course for the final in Baku, with both sides set to avoid each other if they make it through next week's second legs.
Arsenal were all over Napoli from the kick-off and got their deserved opener with 14 minutes on the clock, Ramsay waltzing in at the end of a beautiful passing move to calmly stroke home Ainsley Maitland-Niles's neat lay-off.
Napoli were completely out of sorts, barely able to get the ball out of their own half at times, and 10 minutes later the Gunners doubled their lead.
Former Sampdoria midfielder Lucas Torreira won possession in midfield and charged towards goal before letting off a weak shot that flicked off Koulibaly and flew past a bamboozled Alex Meret in the Napoli goal.
Arsenal should have made more of their first-half dominance over Carlo Ancelotti's slipshod side, but were not punished by the Serie A outfit, who through Piotr Zielinski should have bagged an away goal to take back to Naples in the second half.
"I was surprised by the lack of courage and personality from my players at the start," Carlo Ancelotti told Sky Sport.
"Turning this around will be difficult now, but we'll be home at the San Paolo, and our supporters will help us."
- Record-breaking Felix -
Arsenal will almost certainly take on Valencia should they hold on at what will be an intimidating Stadio San Paolo after the La Liga side scored twice in stoppage time to win 3-1 at fellow Spaniards Villarreal.
Goncalo Guedes scored twice, including what could be the decisive third three minutes into added time, as Marcelino's side struck with two clinical breakaway goals to give them a great chance of making the semis.
Chelsea meanwhile will likely play Benfica should they go through after 19-year-old Joao Felix became the youngest ever player to score a Europa League hat-trick and set up the other goal in 4-2 win over Eintracht Frankfurt that leaves the Bundesliga side, who had to play with 10 men for 70 minutes, with an uphill task to make the last four in Germany next week.
Felix, a revelation in his first season in the Benfica first team, got the ball rolling from the spot in the 21st minute after Evan N'Dicka was sent off for shoving over goal-bound Gedson Fernandes.
He put the hosts back in front just before the break after Luka Jovic -- on loan from Benfica -- scored a shock leveller against his parent club in the 40th minute.
Ruben Dias made it three when he headed in Felix's flick-on a from a corner, and the 19-year-old side-footed home Alex Grimaldo's cross to complete his treble nine minutes into the second half, before Goncalo Paciencia pulled one back with his head from a corner to keep the tie alive.