The duo went a combined 5-for-32 from the field, but their teammates picked them up and both players made key plays down the stretch as IN (40-28) picked up a 101-98 victory over the 76ers (36-30).
The win allowed the Blue & Gold to remain in the third place in the Eastern Conference standings.
The Sixers early lead was short lived as the Pacers, led by Myles Turner, quickly took command.
However, he broke from the norm on Tuesday before losing a key game to the Indiana Pacers, 101-98, at Wells Fargo Center.
Turner led all scorers in the first half with 16 points for the Pacers.
The Sixers stayed within striking distance of the Pacers, as IN held a seven point lead halfway through the fourth quarter. The Blue & Gold took a 57-53 advantage into the break. Embiid missed a three-pointer, and that was it. The Pacers' captain scored seven unanswered points over the next three possessions, the lion's share of what wound up being a 9-0 IN run. Sabonis had to be helped to the locker room - where he was diagnosed with a sprained left ankle - and did not return. Chaos ensued - Pacers' Victor Oladipo was called for an offensive foul and the Sixers got the ball back, a chance to tie, with 7.6 seconds remaining.
Pacers: Booker, who averaged 4.7 points and 3.7 rebounds in 33 games with the 76ers this season before signing with in on March 3, had five points and six rebounds in 17 minutes.
Philly made one last run in the final two minutes, using a J.J. Redick 3-pointer and Embiid layup to make it a 99-96 game with 46 seconds to play.
Threes from Dario Saric, J.J. Redick, and Marco Belinelli pulled the Sixers within four as the Pacers held a 42-38 lead.
With 21 seconds left in the game, the Pacers went up by five points on two free throws.
But Embiid got a dunk on the other end and then Oladipo was whistled for an offensive foul for hooking his arm around Ben Simmons with 7.6 seconds remaining. Out of a timeout, Embiid had a look to tie the game, but missed his shot and Šarić and Oladipo grabbed the rebound simultaneously, resulting in a jump ball with three seconds to play.
Oladipo won the tip to Bogdanovic on the baseline, who threw the ball off of Simmons to put the finishing touches on the victory. This time the Pacers went on a 14-0 run to stretch the lead as large as 25-14. The Pacers opened up a 12-point lead on Lance Stephenson's 18-foot jumper with 10 minutes, 37 seconds left in second quarter.
Meanwhile, Sixers point guard Ben Simmons had 10 points, 13 rebounds and 10 assists (both game highs) for his seventh triple-double of the season.
Joel Embiid had 29 points and 12 rebounds but committed eight turnovers for the Sixers.
Simmons recorded a triple-double in the loss, finishing with 10 points, 13 rebounds, and 10 assists.
Elsewhere, the Los Angeles Clippers retained their place in a play-offs spot with a 112-106 win over the Chicago Bulls while the Dallas Mavericks defeated the New York Knicks 110-97.