Countries worldwide are transforming their energy systems to achieve Carbon-Neutrality. Investing in renewable resources-based technologies and implementing Carbon Capture and Storage (CCS) are common strategies to achieve higher sequestration levels. Negative emissions through Bioenergy with CCS are expected to play an essential role in the transition to full decarbonization. On top of that, biomass is a limited resource that depends on environmental factors, which create uncertainties related to the amount that can be sustainably provided to the energy system. Therefore, this study emphasizes the relevance of variability in carbon sequestration for achieving climate targets by 2050. This paper proposes a probabilistic approach that integrates the Global Change Analysis Model for Latin America (GCAM-LA) with a chance constraint approach. GCAM-LA is used to assess the impact on the energy sector of different limits of sustainable biomass and carbon budget scenarios. The risk associated with exceeding the sequestration capacity of a given region is modeled via Chance Constraint. Results show that electrification is an appropriate long-term decarbonization strategy. It smoothes the effects of uncertainty in sequestration capacity and responds to end-user demands. For this case study, higher levels of electrification are obtained at likelihood levels >66% for end-use sectors.