The midfielder was replaced by Peter Haring in the 86th minute with a knee complaint after a long stoppage.
Despite the presence of a stretcher, Baningime responded well after the match and Neilson thinks he will be available for selection with a trip to Parkhead coming up during the week before a fixture at Livingston on Sunday.
“I think he’s alright," he said. “He’s up and walking about, has had a shower.
"I think he just got more of a shock at the time, he kind of twisted his knee a wee bit.
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"The physio goes on and he gets stretchered off. He’ll be getting a bit of stick tomorrow if he trains.
“When you see someone get stretchered off you are a wee bit unsure. Even when he came off he said he was orite.
Neilson added: “I think he just wanted a standing ovation.”
St Mirren made it tough for Hearts before Gary Mackay-Steven gave the home side the lead which was reflected in the frustration from the crowd at half-time and during the second half when the team were under pressure.
Once the home side went in front there was a confidence to the play and the team could have added further to the scoresheet.
"That is part and parcel of playing at Tynecastle," Neilson said. “You pay your money to get entertained, to see goals, to see shots at goal.
"I thought they pressed us well in the first half and when we got into areas we didn’t have that final moment, the chance to pull the trigger we didn’t do it.
"The second half we were a lot more free flowing.
“St Mirren are a very good team. They press really well, they get in and stop you trying to play and then they’ve got three players up front that can really influence the game in [Eamonn] Brophy, [Jamie] McGrath and [Connor] Ronan so they are a threat.
"I think they will take points off a lot of teams over a lot of games this season. We knew in the first half they would come and do that and then it's up to us to try and play through it.
"In these games the first goal is always going to be key, we managed to get it, they open up and we can go and play.”
He added: “For us it’s about winning games. We’ve been doing really well at Tynecastle, it’s now about taking it to away games and the next away game is Tynecastle.”
The three points which lifted Hearts into third for the time being was confirmed by a fantastic free-kick from Stephen Kingsley who netted his fourth goal of the season.
He may well have added another late on following a red card to Joe Shaughnessy but he sent his second attempt flying over the bar.
To Neilson it was no surprise when the ball hit the back of the net.
“To be fair he practices all the time," he said. “He’s got real quality in that left foot.”