- Manager Slaven Bilic's fourth game in charge
- Birkirkara are Maltese Cup winners
- Modibo Maiga has goal ruled out for offside
- Hammers face Romanian side Astra next
West Ham scraped through to the Europa League third qualifying round but required penalties to get past Maltese side Birkirkara.
The Hammers led 1-0 after the first leg, but striker Fabrizio Miccoli slid in to equalise on aggregate.
In a bad-tempered game, both sides had a man sent off, the Hammers' James Tomkins for pushing Nikola Vukanac, and Mauricio Mazzetti for the Maltese side.
The Hammers scored all five spot-kicks, Diego Poyet notching the decisive one.
West Ham will now face Romanian side Astra - who knocked out Scottish Premiership side Inverness Caledonian Thistle - and still need to negotiate their way through that two-legged tie plus a play-off round to reach the group stages.
None of the club's seven summer signings played, while Enner Valencia and Winston Reid were also missing at Ta' Qali National Stadium.
Slaven Bilic's side struggled against Birkirkara - the Maltese Cup winners, ranked 360th on the Uefa coefficients list.
The hosts tackled hard and frustrated their opponents, with former Italy international Miccoli and midfielder Mark Noble both booked after a heated exchange.
Further controversy followed on half-time when centre-back Tomkins was sent off after grabbing Vukanac and throwing the defender to the ground as they jostled before a Hammers corner. The referee waited for the ensuing scuffle to clear before showing Vukanac a yellow card and Tomkins, who scored the only goal last week, red.
West ham created virtually nothing, although winger Matt Jarvis had a low drive smothered by goalkeeper Justin Haber - his team's only shot on target in the match.
At the other end, they were punished as Brazilian forward Liliu drilled in a low cross which Miccoli converted after beating Joey O'Brien to the ball.
The impressive defender Mazzetti was dismissed with 12 minutes remaining for a second booking and West Ham substitute Modibo Maiga had a late goal ruled out for offside.
But after struggling in the heat, the Londoners kept their cool during the penalty shootout.
- 15VukanacBooked at 45mins
- 5MazzettiBooked at 107mins
- 24MuscatSubstituted forAgiusat 71'minutesBooked at 111mins
- 2EmersonSubstituted forZammitat 97'minutes
- 10MiccoliBooked at 33minsSubstituted forPlutat 77'minutesBooked at 86mins
- 17O'BrienBooked at 18mins
- 19CollinsBooked at 108mins
- 5TomkinsBooked at 45mins
- 16NobleBooked at 33mins
- 21AmalfitanoSubstituted forMaigaat 60'minutes
- 4NolanSubstituted forPoyetat 59'minutes
- 7JarvisSubstituted forSamuelsenat 120'minutes
- Enea Jorgji
- Shots on Target