Two headed goals from corner kicks seven minutes apart by central defenders Jose Maria Gimenez and Saul put Atletico on track after Keko had given Eibar the lead in the 46th.
Coach Diego Simeone will be glad his side ended a run of four matches without a win in La Liga and the King's Cup while Torres, who netted in added time, had been waiting since a victory at Eibar in September to reach his century for the club.
Atletico are unlikely to stay joint top on 51 points beyond Sunday as rampant Barcelona, who have a better goal difference and two matches in hand, visit bottom team Levante.
Real Madrid, away to Granada on Sunday, are in third place, four points off the pace.
Torres' much-celebrated goal was the icing on the cake for Atletico.
"To score my 100th goal is a prize for my career," said Torres, back at his first club after playing for Liverpool, Chelsea and AC Milan.
Simeone also reached 100 wins in 159 La Liga matches in charge of Atletico and had to thank his defenders in a revamped back four, after last weekend's costly 2-1 defeat at Barcelona, for the victory.
Atletico were minus the suspended Diego Godin, Felipe Luis and Juanfran, with only Gimenez remaining from the side that played at the Nou Camp.
The second half had barely got underway when Saul slipped in the box, allowing Sergi Enrich to set up Keko who curled the ball into the top corner.
Ten minutes later Eibar goalkeeper Asier Riesgo saved from Saul but gave away a corner and Gimenez rose to power a header into the net.
Saul then scored a near carbon-copy goal to put Atletico ahead and the substitutions Simeone made in the final 20 minutes put Eibar on the back foot.
Luciano Vietto, who replaced fellow Argentine Angel Correa, had a goal disallowed in the 75th minute for offside before Torres put his first chance wide in the 81st.
Villarreal drew 0-0 in a bad-tempered encounter at fellow European hopefuls Athletic Bilbao.
Inaki Williams (Bilbao) and Daniele Bonera (Villarreal) were both dismissed late on.
Jony scored the 600th goal of the season in La Liga as Sporting Gijon drew 1-1 with Deportivo La Coruna who replied through Luis Alberto.
Rayo Vallecano beat Las Palmas 2-0 to climb out of the relegation zone.
(Writing by Rex Gowar; editing by Clare Fallon)
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