The Giallorossi conceded early goals in each half and ultimately paid the price, despite Daniele De Rossi's equaliser on the stroke of half-time.
Keita Balde had opened the scoring for the day's visitors and five minutes after the restart it was Dusan Basta who put Lazio back ahead, as his wickedly deflected strike crept beyond Wojciech Szczesny.
Luciano Spalletti's side pushed forward desperately for an equaliser but, despite the addition of Francesco Totti with 20 minutes remaining, struggled to create clear-cut openings.
Lazio continued to look dangerous on the counter-attack, and with five minutes remaining it was Keita who finished the game with his second goal of the game.
Roma remain second in the Serie A standings, albeit now nine points behind leaders Juventus with four games remaining.
After sitting on the bench for Monday's win Pescara, Daniele De Rossi returned to midfield for this game - and consequently also wore the captain's armband.
Elsewhere Spalletti stuck with the 4-2-3-1 formation he has used in recent weeks - with Radja Nainggolan, Stephan El Shaarawy and Mohamed Salah supporting Edin Dzeko.
2' - First chance! Strootman plays in Dzeko, who controls well and then fires a shot Strakosha has to tip over!
9' - SAVE! A solo run from Salah sees him escape the defence and get a shot off - but Strakosha makes a finger-tip save!
12' - Goal. Lazio lead. Keita Balde cuts inside onto his left and fires into the bottom corner. 0-1.
36' - Szczesny makes a good save to palm away Parolo's long-range drive on the counter.
45' - PENALTY! Wallace fouls Strootman in the box!
45' - GOAL! ROMA LEVEL! Captain De Rossi takes on the responsibility himself ... and rolls his shot low to the keeper's left to put his side level again! 1-1!
See more images in our dedicated match gallery.
48' - CLOSE! Salah does brilliantly to get in behind and feed Dzeko, but Strakosha pulls off a remarkable save!
50' - Goal. Lazio lead again. Basta's deflected strike creeps in off the inside of the post. 1-2.
63' - Felipe Anderson's shot from an acute angle is prodded away by Szczesny.
76' - Emerson goes for the spectacular, but his shot is always high and rising.
82' - Important save from Szczesny - he denies Felipe Anderson one-on-one to keep Roma in it.
85' - Goal. Lulic breaks clear on the counter and then feeds Keita for the finish. 1-3.
90' - Red card for Rudiger after a foul on Djordjevic.
See more game statistics in our dedicated match centre.
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"Today we have to swallow the analysis that will be made about us: we lost focus and we probably made some wrong decisions at points. We had two more clear goalscoring chances compared to them, but instead of nicking deflections we could only find saves from their keeper. This is what made the difference."Obviously, after their goal, our confidence dropped and we lost grip on our game plan. Nevertheless, the match hinged on the blow against the run of play."
- Luciano Spalletti
The Giallorossi are next in action in seven days, as they travel to Milan to face AC Milan on Sunday evening.
The next game at the Stadio Olimpico is against Juventus on May 14.
Goalscorers: De Rossi (45' p.); Keita (12', 85'), Basta (50')
Roma: Szczesny; Emerson, Fazio (Perotti), Manolas, Rudiger; Strootman, De Rossi (Totti); El Shaarawy (Peres), Nainggolan, Salah; Dzeko.
Lazio: Strakosha; Bastos, de Vrij, Wallace, Lukaku; Basta, Parolo, Biglia, Milinkovic, Lulic; Keita.
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