Barry already knew he could increase his metabolic activity because of his inability to get drunk on alcohol. He learned this a few episodes ago.
It is a perfectly reasonable assumption that like he, a learned scientist would make that like an engine, if he ran hotter, he would use more fuel and amp his metabolic process enough to get rid of the tranquilizer.
We also saw in his last episode he had been supercharged by the electrical-powered metahuman, "Blackout" and was now charged even higher than he was before. It is possible he may not even realize he is able to do more powerful feats such as phasing (if indeed this is what he did.)
In the episode recap of "Power Outage" by GotchaMovies:
Barry now faces off against Farooq once again, and eventually gets siphoned by him. This time however, Farooq's power overloads which causes him to have a meltdown and die.
The group is left puzzled as to why, but discover that the experiment used to give Barry his powers back supercharged his cells to make him faster and stronger than ever.
Farooq simply could not handle all the power inside of Barry's body and met his fatal end because of it. Farooq's body is dumped inside one of the cells just in case he ever returns. Cisco is disappointed Farooq died because he wanted to give him the name "Blackout".
"Look, this is a sample of your blood from just after you were struck by lightning." (The energy representation is silver and energetically moving.)
"Now your cells are generating more energy than ever before. It was more energy than the meta could safely handle. It's almost like he choked on you." (The energy representation is now golden and even more energetic.)
In the comics, Barry was known for experimenting with his powers on the fly, learning by doing. When you are the fastest man alive, trial and error can be implemented, learned from and corrected, in a Flash...